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IMP Reference Guide  develop.23016263b1,2026/04/24
The Integrative Modeling Platform
bff/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.4.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2026 IMP Inventors. All rights reserved.
10 
11 
12 
13 
14 from sys import version_info as _swig_python_version_info
15 import _IMP_bff
16 
17 try:
18  import builtins as __builtin__
19 except ImportError:
20  import __builtin__
21 
22 def _swig_repr(self):
23  try:
24  strthis = "proxy of " + self.this.__repr__()
25  except __builtin__.Exception:
26  strthis = ""
27  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
28 
29 
30 def _swig_setattr_nondynamic_instance_variable(set):
31  def set_instance_attr(self, name, value):
32  if name == "this":
33  set(self, name, value)
34  elif name == "thisown":
35  self.this.own(value)
36  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
37  set(self, name, value)
38  else:
39  raise AttributeError("You cannot add instance attributes to %s" % self)
40  return set_instance_attr
41 
42 
43 def _swig_setattr_nondynamic_class_variable(set):
44  def set_class_attr(cls, name, value):
45  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
46  set(cls, name, value)
47  else:
48  raise AttributeError("You cannot add class attributes to %s" % cls)
49  return set_class_attr
50 
51 
52 def _swig_add_metaclass(metaclass):
53  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
54  def wrapper(cls):
55  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
56  return wrapper
57 
58 
59 class _SwigNonDynamicMeta(type):
60  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
61  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
62 
63 
64 import weakref
65 
66 class IMP_BFF_SwigPyIterator(object):
67  r"""Proxy of C++ swig::IMP_BFF_SwigPyIterator class."""
68 
69  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
70 
71  def __init__(self, *args, **kwargs):
72  raise AttributeError("No constructor defined - class is abstract")
73  __repr__ = _swig_repr
74  __swig_destroy__ = _IMP_bff.delete_IMP_BFF_SwigPyIterator
75 
76  def value(self):
77  r"""value(IMP_BFF_SwigPyIterator self) -> PyObject *"""
78  return _IMP_bff.IMP_BFF_SwigPyIterator_value(self)
79 
80  def incr(self, n=1):
81  r"""incr(IMP_BFF_SwigPyIterator self, size_t n=1) -> IMP_BFF_SwigPyIterator"""
82  return _IMP_bff.IMP_BFF_SwigPyIterator_incr(self, n)
83 
84  def decr(self, n=1):
85  r"""decr(IMP_BFF_SwigPyIterator self, size_t n=1) -> IMP_BFF_SwigPyIterator"""
86  return _IMP_bff.IMP_BFF_SwigPyIterator_decr(self, n)
87 
88  def distance(self, x):
89  r"""distance(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> ptrdiff_t"""
90  return _IMP_bff.IMP_BFF_SwigPyIterator_distance(self, x)
91 
92  def equal(self, x):
93  r"""equal(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> bool"""
94  return _IMP_bff.IMP_BFF_SwigPyIterator_equal(self, x)
95 
96  def copy(self):
97  r"""copy(IMP_BFF_SwigPyIterator self) -> IMP_BFF_SwigPyIterator"""
98  return _IMP_bff.IMP_BFF_SwigPyIterator_copy(self)
99 
100  def next(self):
101  r"""next(IMP_BFF_SwigPyIterator self) -> PyObject *"""
102  return _IMP_bff.IMP_BFF_SwigPyIterator_next(self)
103 
104  def __next__(self):
105  r"""__next__(IMP_BFF_SwigPyIterator self) -> PyObject *"""
106  return _IMP_bff.IMP_BFF_SwigPyIterator___next__(self)
107 
108  def previous(self):
109  r"""previous(IMP_BFF_SwigPyIterator self) -> PyObject *"""
110  return _IMP_bff.IMP_BFF_SwigPyIterator_previous(self)
111 
112  def advance(self, n):
113  r"""advance(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator"""
114  return _IMP_bff.IMP_BFF_SwigPyIterator_advance(self, n)
115 
116  def __eq__(self, x):
117  r"""__eq__(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> bool"""
118  return _IMP_bff.IMP_BFF_SwigPyIterator___eq__(self, x)
119 
120  def __ne__(self, x):
121  r"""__ne__(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> bool"""
122  return _IMP_bff.IMP_BFF_SwigPyIterator___ne__(self, x)
123 
124  def __iadd__(self, n):
125  r"""__iadd__(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator"""
126  return _IMP_bff.IMP_BFF_SwigPyIterator___iadd__(self, n)
127 
128  def __isub__(self, n):
129  r"""__isub__(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator"""
130  return _IMP_bff.IMP_BFF_SwigPyIterator___isub__(self, n)
131 
132  def __add__(self, n):
133  r"""__add__(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator"""
134  return _IMP_bff.IMP_BFF_SwigPyIterator___add__(self, n)
135 
136  def __sub__(self, *args):
137  r"""
138  __sub__(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator
139  __sub__(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> ptrdiff_t
140  """
141  return _IMP_bff.IMP_BFF_SwigPyIterator___sub__(self, *args)
142  def __iter__(self):
143  return self
144 
145 # Register IMP_BFF_SwigPyIterator in _IMP_bff:
146 _IMP_bff.IMP_BFF_SwigPyIterator_swigregister(IMP_BFF_SwigPyIterator)
147 
148 _value_types=[]
149 _object_types=[]
150 _raii_types=[]
151 _plural_types=[]
152 
153 IMP_DEBUG = _IMP_bff.IMP_DEBUG
154 
155 IMP_RELEASE = _IMP_bff.IMP_RELEASE
156 
157 IMP_SILENT = _IMP_bff.IMP_SILENT
158 
159 IMP_PROGRESS = _IMP_bff.IMP_PROGRESS
160 
161 IMP_TERSE = _IMP_bff.IMP_TERSE
162 
163 IMP_VERBOSE = _IMP_bff.IMP_VERBOSE
164 
165 IMP_MEMORY = _IMP_bff.IMP_MEMORY
166 
167 IMP_NONE = _IMP_bff.IMP_NONE
168 
169 IMP_USAGE = _IMP_bff.IMP_USAGE
170 
171 IMP_INTERNAL = _IMP_bff.IMP_INTERNAL
172 
173 IMP_KERNEL_HAS_LOG4CXX = _IMP_bff.IMP_KERNEL_HAS_LOG4CXX
174 
175 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_bff.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
176 
177 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_bff.IMP_COMPILER_HAS_DEBUG_VECTOR
178 
179 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_bff.IMP_COMPILER_HAS_RANDOM_SHUFFLE
180 
181 IMP_COMPILER_HAS_THREE_WAY = _IMP_bff.IMP_COMPILER_HAS_THREE_WAY
182 
183 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_bff.IMP_KERNEL_HAS_BOOST_RANDOM
184 
185 IMP_KERNEL_HAS_NUMPY = _IMP_bff.IMP_KERNEL_HAS_NUMPY
186 
187 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_bff.IMP_KERNEL_HAS_BOOST_SYSTEM
188 
189 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_bff.IMP_KERNEL_HAS_GPERFTOOLS
190 
191 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_bff.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 
193 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_bff.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 
195 IMPKERNEL_SHOW_WARNINGS = _IMP_bff.IMPKERNEL_SHOW_WARNINGS
196 
197 
198 import sys
199 class _DirectorObjects:
200  """@internal Simple class to keep references to director objects
201  to prevent premature deletion."""
202  def __init__(self):
203  self._objects = []
204  def register(self, obj):
205  """Take a reference to a director object; will only work for
206  refcounted C++ classes"""
207  if hasattr(obj, 'get_ref_count'):
208  self._objects.append(obj)
209  def cleanup(self):
210  """Only drop our reference and allow cleanup by Python if no other
211  Python references exist (we hold 3 references: one in self._objects,
212  one in x, and one in the argument list for getrefcount) *and* no
213  other C++ references exist (the Python object always holds one)"""
214  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
215  or x.get_ref_count() > 1]
216 # Do in two steps so the references are kept until the end of the
217 # function (deleting references may trigger a fresh call to this method)
218  self._objects = objs
219  def get_object_count(self):
220  """Get number of director objects (useful for testing only)"""
221  return len(self._objects)
222 _director_objects = _DirectorObjects()
223 
224 class _ostream(object):
225  r"""Proxy of C++ std::ostream class."""
226 
227  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
228 
229  def __init__(self, *args, **kwargs):
230  raise AttributeError("No constructor defined")
231  __repr__ = _swig_repr
232 
233  def write(self, osa_buf):
234  r"""write(_ostream self, char const * osa_buf)"""
235  return _IMP_bff._ostream_write(self, osa_buf)
236 
237 # Register _ostream in _IMP_bff:
238 _IMP_bff._ostream_swigregister(_ostream)
239 IMP_C_OPEN_BINARY = _IMP_bff.IMP_C_OPEN_BINARY
240 
241 import IMP
242 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 
244 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 
246 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_bff.IMP_CGAL_HAS_BOOST_RANDOM
247 
248 IMP_CGAL_HAS_NUMPY = _IMP_bff.IMP_CGAL_HAS_NUMPY
249 
250 IMPCGAL_SHOW_WARNINGS = _IMP_bff.IMPCGAL_SHOW_WARNINGS
251 
252 import IMP.cgal
253 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_bff.IMP_ALGEBRA_HAS_IMP_CGAL
254 
255 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
256 
257 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
258 
259 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_bff.IMP_ALGEBRA_HAS_BOOST_RANDOM
260 
261 IMP_ALGEBRA_HAS_CGAL = _IMP_bff.IMP_ALGEBRA_HAS_CGAL
262 
263 IMP_ALGEBRA_HAS_NUMPY = _IMP_bff.IMP_ALGEBRA_HAS_NUMPY
264 
265 IMP_ALGEBRA_HAS_ANN = _IMP_bff.IMP_ALGEBRA_HAS_ANN
266 
267 IMPALGEBRA_SHOW_WARNINGS = _IMP_bff.IMPALGEBRA_SHOW_WARNINGS
268 
269 import IMP.algebra
270 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_bff.IMP_DISPLAY_HAS_IMP_CGAL
271 
272 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
273 
274 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
275 
276 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_bff.IMP_DISPLAY_HAS_BOOST_RANDOM
277 
278 IMP_DISPLAY_HAS_CGAL = _IMP_bff.IMP_DISPLAY_HAS_CGAL
279 
280 IMP_DISPLAY_HAS_NUMPY = _IMP_bff.IMP_DISPLAY_HAS_NUMPY
281 
282 IMPDISPLAY_SHOW_WARNINGS = _IMP_bff.IMPDISPLAY_SHOW_WARNINGS
283 
284 import IMP.display
285 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
286 
287 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
288 
289 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
290 
291 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
292 
293 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_CGAL
294 
295 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_HDF5
296 
297 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_NUMPY
298 
299 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_bff.IMPSCOREFUNCTOR_SHOW_WARNINGS
300 
301 import IMP.score_functor
302 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_bff.IMP_STATISTICS_HAS_IMP_CGAL
303 
304 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
305 
306 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
307 
308 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_bff.IMP_STATISTICS_HAS_BOOST_RANDOM
309 
310 IMP_STATISTICS_HAS_CGAL = _IMP_bff.IMP_STATISTICS_HAS_CGAL
311 
312 IMP_STATISTICS_HAS_NUMPY = _IMP_bff.IMP_STATISTICS_HAS_NUMPY
313 
314 IMPSTATISTICS_SHOW_WARNINGS = _IMP_bff.IMPSTATISTICS_SHOW_WARNINGS
315 
316 import IMP.statistics
317 IMP_CORE_HAS_IMP_CGAL = _IMP_bff.IMP_CORE_HAS_IMP_CGAL
318 
319 IMP_CORE_HAS_IMP_KERNEL = _IMP_bff.IMP_CORE_HAS_IMP_KERNEL
320 
321 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_CORE_HAS_BOOST_FILESYSTEM
322 
323 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
324 
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_bff.IMP_CORE_HAS_BOOST_RANDOM
326 
327 IMP_CORE_HAS_CGAL = _IMP_bff.IMP_CORE_HAS_CGAL
328 
329 IMP_CORE_HAS_HDF5 = _IMP_bff.IMP_CORE_HAS_HDF5
330 
331 IMP_CORE_HAS_NUMPY = _IMP_bff.IMP_CORE_HAS_NUMPY
332 
333 IMPCORE_SHOW_WARNINGS = _IMP_bff.IMPCORE_SHOW_WARNINGS
334 
335 import IMP.core
336 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_bff.IMP_CONTAINER_HAS_IMP_ALGEBRA
337 
338 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_bff.IMP_CONTAINER_HAS_IMP_CGAL
339 
340 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_bff.IMP_CONTAINER_HAS_IMP_DISPLAY
341 
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_bff.IMP_CONTAINER_HAS_IMP_KERNEL
343 
344 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_bff.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
345 
346 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
347 
348 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
349 
350 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_bff.IMP_CONTAINER_HAS_BOOST_RANDOM
351 
352 IMP_CONTAINER_HAS_CGAL = _IMP_bff.IMP_CONTAINER_HAS_CGAL
353 
354 IMP_CONTAINER_HAS_HDF5 = _IMP_bff.IMP_CONTAINER_HAS_HDF5
355 
356 IMP_CONTAINER_HAS_NUMPY = _IMP_bff.IMP_CONTAINER_HAS_NUMPY
357 
358 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_bff.IMP_CONTAINER_HAS_PYTHON_IHM
359 
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_bff.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 
362 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_bff.IMP_CONTAINER_HAS_ROBIN_MAP
363 
364 IMPCONTAINER_SHOW_WARNINGS = _IMP_bff.IMPCONTAINER_SHOW_WARNINGS
365 
366 import IMP.container
367 IMP_ATOM_HAS_IMP_CGAL = _IMP_bff.IMP_ATOM_HAS_IMP_CGAL
368 
369 IMP_ATOM_HAS_IMP_KERNEL = _IMP_bff.IMP_ATOM_HAS_IMP_KERNEL
370 
371 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_bff.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
372 
373 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
374 
375 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_bff.IMP_ATOM_HAS_BOOST_RANDOM
376 
377 IMP_ATOM_HAS_BOOST_REGEX = _IMP_bff.IMP_ATOM_HAS_BOOST_REGEX
378 
379 IMP_ATOM_HAS_CGAL = _IMP_bff.IMP_ATOM_HAS_CGAL
380 
381 IMP_ATOM_HAS_HDF5 = _IMP_bff.IMP_ATOM_HAS_HDF5
382 
383 IMP_ATOM_HAS_NUMPY = _IMP_bff.IMP_ATOM_HAS_NUMPY
384 
385 IMP_ATOM_HAS_PYTHON_IHM = _IMP_bff.IMP_ATOM_HAS_PYTHON_IHM
386 
387 IMPATOM_SHOW_WARNINGS = _IMP_bff.IMPATOM_SHOW_WARNINGS
388 
389 IMP_ATOM_TYPE_INDEX = _IMP_bff.IMP_ATOM_TYPE_INDEX
390 
391 IMP_RESIDUE_TYPE_INDEX = _IMP_bff.IMP_RESIDUE_TYPE_INDEX
392 
393 IMP_HIERARCHY_TYPE_INDEX = _IMP_bff.IMP_HIERARCHY_TYPE_INDEX
394 
395 IMP_CHAIN_TYPE_INDEX = _IMP_bff.IMP_CHAIN_TYPE_INDEX
396 
397 import IMP.atom
398 IMP_EM_HAS_IMP_CGAL = _IMP_bff.IMP_EM_HAS_IMP_CGAL
399 
400 IMP_EM_HAS_IMP_CONTAINER = _IMP_bff.IMP_EM_HAS_IMP_CONTAINER
401 
402 IMP_EM_HAS_IMP_DISPLAY = _IMP_bff.IMP_EM_HAS_IMP_DISPLAY
403 
404 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_bff.IMP_EM_HAS_IMP_SCORE_FUNCTOR
405 
406 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_EM_HAS_BOOST_FILESYSTEM
407 
408 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
409 
410 IMP_EM_HAS_BOOST_RANDOM = _IMP_bff.IMP_EM_HAS_BOOST_RANDOM
411 
412 IMP_EM_HAS_BOOST_REGEX = _IMP_bff.IMP_EM_HAS_BOOST_REGEX
413 
414 IMP_EM_HAS_CGAL = _IMP_bff.IMP_EM_HAS_CGAL
415 
416 IMP_EM_HAS_HDF5 = _IMP_bff.IMP_EM_HAS_HDF5
417 
418 IMP_EM_HAS_NUMPY = _IMP_bff.IMP_EM_HAS_NUMPY
419 
420 IMP_EM_HAS_PYTHON_IHM = _IMP_bff.IMP_EM_HAS_PYTHON_IHM
421 
422 IMPEM_SHOW_WARNINGS = _IMP_bff.IMPEM_SHOW_WARNINGS
423 
424 import IMP.em
425 IMP_BFF_HAS_IMP_ALGEBRA = _IMP_bff.IMP_BFF_HAS_IMP_ALGEBRA
426 
427 IMP_BFF_HAS_IMP_CGAL = _IMP_bff.IMP_BFF_HAS_IMP_CGAL
428 
429 IMP_BFF_HAS_IMP_DISPLAY = _IMP_bff.IMP_BFF_HAS_IMP_DISPLAY
430 
431 IMP_BFF_HAS_IMP_KERNEL = _IMP_bff.IMP_BFF_HAS_IMP_KERNEL
432 
433 IMP_BFF_HAS_IMP_SCORE_FUNCTOR = _IMP_bff.IMP_BFF_HAS_IMP_SCORE_FUNCTOR
434 
435 IMP_BFF_HAS_IMP_STATISTICS = _IMP_bff.IMP_BFF_HAS_IMP_STATISTICS
436 
437 IMP_BFF_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_BFF_HAS_BOOST_FILESYSTEM
438 
439 IMP_BFF_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_BFF_HAS_BOOST_PROGRAMOPTIONS
440 
441 IMP_BFF_HAS_BOOST_RANDOM = _IMP_bff.IMP_BFF_HAS_BOOST_RANDOM
442 
443 IMP_BFF_HAS_BOOST_REGEX = _IMP_bff.IMP_BFF_HAS_BOOST_REGEX
444 
445 IMP_BFF_HAS_CGAL = _IMP_bff.IMP_BFF_HAS_CGAL
446 
447 IMP_BFF_HAS_HDF5 = _IMP_bff.IMP_BFF_HAS_HDF5
448 
449 IMP_BFF_HAS_PYTHON_IHM = _IMP_bff.IMP_BFF_HAS_PYTHON_IHM
450 
451 IMP_BFF_HAS_AVX = _IMP_bff.IMP_BFF_HAS_AVX
452 
453 IMPBFF_SHOW_WARNINGS = _IMP_bff.IMPBFF_SHOW_WARNINGS
454 
455 
456 import numpy as np
457 
458 SHARED_PTR_DISOWN = _IMP_bff.SHARED_PTR_DISOWN
459 
460 class PairFloatFloat(object):
461  r"""Proxy of C++ std::pair< float,float > class."""
462 
463  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
464  __repr__ = _swig_repr
465 
466  def __init__(self, *args):
467  r"""
468  __init__(PairFloatFloat self) -> PairFloatFloat
469  __init__(PairFloatFloat self, float first, float second) -> PairFloatFloat
470  __init__(PairFloatFloat self, PairFloatFloat other) -> PairFloatFloat
471  """
472  _IMP_bff.PairFloatFloat_swiginit(self, _IMP_bff.new_PairFloatFloat(*args))
473  first = property(_IMP_bff.PairFloatFloat_first_get, _IMP_bff.PairFloatFloat_first_set, doc=r"""first : float""")
474  second = property(_IMP_bff.PairFloatFloat_second_get, _IMP_bff.PairFloatFloat_second_set, doc=r"""second : float""")
475  def __len__(self):
476  return 2
477  def __repr__(self):
478  return str((self.first, self.second))
479  def __getitem__(self, index):
480  if not (index % 2):
481  return self.first
482  else:
483  return self.second
484  def __setitem__(self, index, val):
485  if not (index % 2):
486  self.first = val
487  else:
488  self.second = val
489  __swig_destroy__ = _IMP_bff.delete_PairFloatFloat
490 
491 # Register PairFloatFloat in _IMP_bff:
492 _IMP_bff.PairFloatFloat_swigregister(PairFloatFloat)
493 class VectorString(object):
494  r"""Proxy of C++ std::vector< std::string > class."""
495 
496  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
497  __repr__ = _swig_repr
498 
499  def iterator(self):
500  r"""iterator(VectorString self) -> IMP_BFF_SwigPyIterator"""
501  return _IMP_bff.VectorString_iterator(self)
502  def __iter__(self):
503  return self.iterator()
504 
505  def __nonzero__(self):
506  r"""__nonzero__(VectorString self) -> bool"""
507  return _IMP_bff.VectorString___nonzero__(self)
508 
509  def __bool__(self):
510  r"""__bool__(VectorString self) -> bool"""
511  return _IMP_bff.VectorString___bool__(self)
512 
513  def __len__(self):
514  r"""__len__(VectorString self) -> std::vector< std::string >::size_type"""
515  return _IMP_bff.VectorString___len__(self)
516 
517  def __getslice__(self, i, j):
518  r"""__getslice__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::difference_type j) -> VectorString"""
519  return _IMP_bff.VectorString___getslice__(self, i, j)
520 
521  def __setslice__(self, *args):
522  r"""
523  __setslice__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::difference_type j)
524  __setslice__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::difference_type j, VectorString v)
525  """
526  return _IMP_bff.VectorString___setslice__(self, *args)
527 
528  def __delslice__(self, i, j):
529  r"""__delslice__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::difference_type j)"""
530  return _IMP_bff.VectorString___delslice__(self, i, j)
531 
532  def __delitem__(self, *args):
533  r"""
534  __delitem__(VectorString self, std::vector< std::string >::difference_type i)
535  __delitem__(VectorString self, SWIGPY_SLICEOBJECT * slice)
536  """
537  return _IMP_bff.VectorString___delitem__(self, *args)
538 
539  def __getitem__(self, *args):
540  r"""
541  __getitem__(VectorString self, SWIGPY_SLICEOBJECT * slice) -> VectorString
542  __getitem__(VectorString self, std::vector< std::string >::difference_type i) -> std::vector< std::string >::value_type const &
543  """
544  return _IMP_bff.VectorString___getitem__(self, *args)
545 
546  def __setitem__(self, *args):
547  r"""
548  __setitem__(VectorString self, SWIGPY_SLICEOBJECT * slice, VectorString v)
549  __setitem__(VectorString self, SWIGPY_SLICEOBJECT * slice)
550  __setitem__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::value_type const & x)
551  """
552  return _IMP_bff.VectorString___setitem__(self, *args)
553 
554  def pop(self):
555  r"""pop(VectorString self) -> std::vector< std::string >::value_type"""
556  return _IMP_bff.VectorString_pop(self)
557 
558  def append(self, x):
559  r"""append(VectorString self, std::vector< std::string >::value_type const & x)"""
560  return _IMP_bff.VectorString_append(self, x)
561 
562  def empty(self):
563  r"""empty(VectorString self) -> bool"""
564  return _IMP_bff.VectorString_empty(self)
565 
566  def size(self):
567  r"""size(VectorString self) -> std::vector< std::string >::size_type"""
568  return _IMP_bff.VectorString_size(self)
569 
570  def swap(self, v):
571  r"""swap(VectorString self, VectorString v)"""
572  return _IMP_bff.VectorString_swap(self, v)
573 
574  def begin(self):
575  r"""begin(VectorString self) -> std::vector< std::string >::iterator"""
576  return _IMP_bff.VectorString_begin(self)
577 
578  def end(self):
579  r"""end(VectorString self) -> std::vector< std::string >::iterator"""
580  return _IMP_bff.VectorString_end(self)
581 
582  def rbegin(self):
583  r"""rbegin(VectorString self) -> std::vector< std::string >::reverse_iterator"""
584  return _IMP_bff.VectorString_rbegin(self)
585 
586  def rend(self):
587  r"""rend(VectorString self) -> std::vector< std::string >::reverse_iterator"""
588  return _IMP_bff.VectorString_rend(self)
589 
590  def clear(self):
591  r"""clear(VectorString self)"""
592  return _IMP_bff.VectorString_clear(self)
593 
594  def get_allocator(self):
595  r"""get_allocator(VectorString self) -> std::vector< std::string >::allocator_type"""
596  return _IMP_bff.VectorString_get_allocator(self)
597 
598  def pop_back(self):
599  r"""pop_back(VectorString self)"""
600  return _IMP_bff.VectorString_pop_back(self)
601 
602  def erase(self, *args):
603  r"""
604  erase(VectorString self, std::vector< std::string >::iterator pos) -> std::vector< std::string >::iterator
605  erase(VectorString self, std::vector< std::string >::iterator first, std::vector< std::string >::iterator last) -> std::vector< std::string >::iterator
606  """
607  return _IMP_bff.VectorString_erase(self, *args)
608 
609  def __init__(self, *args):
610  r"""
611  __init__(VectorString self) -> VectorString
612  __init__(VectorString self, VectorString other) -> VectorString
613  __init__(VectorString self, std::vector< std::string >::size_type size) -> VectorString
614  __init__(VectorString self, std::vector< std::string >::size_type size, std::vector< std::string >::value_type const & value) -> VectorString
615  """
616  _IMP_bff.VectorString_swiginit(self, _IMP_bff.new_VectorString(*args))
617 
618  def push_back(self, x):
619  r"""push_back(VectorString self, std::vector< std::string >::value_type const & x)"""
620  return _IMP_bff.VectorString_push_back(self, x)
621 
622  def front(self):
623  r"""front(VectorString self) -> std::vector< std::string >::value_type const &"""
624  return _IMP_bff.VectorString_front(self)
625 
626  def back(self):
627  r"""back(VectorString self) -> std::vector< std::string >::value_type const &"""
628  return _IMP_bff.VectorString_back(self)
629 
630  def assign(self, n, x):
631  r"""assign(VectorString self, std::vector< std::string >::size_type n, std::vector< std::string >::value_type const & x)"""
632  return _IMP_bff.VectorString_assign(self, n, x)
633 
634  def resize(self, *args):
635  r"""
636  resize(VectorString self, std::vector< std::string >::size_type new_size)
637  resize(VectorString self, std::vector< std::string >::size_type new_size, std::vector< std::string >::value_type const & x)
638  """
639  return _IMP_bff.VectorString_resize(self, *args)
640 
641  def insert(self, *args):
642  r"""
643  insert(VectorString self, std::vector< std::string >::iterator pos, std::vector< std::string >::value_type const & x) -> std::vector< std::string >::iterator
644  insert(VectorString self, std::vector< std::string >::iterator pos, std::vector< std::string >::size_type n, std::vector< std::string >::value_type const & x)
645  """
646  return _IMP_bff.VectorString_insert(self, *args)
647 
648  def reserve(self, n):
649  r"""reserve(VectorString self, std::vector< std::string >::size_type n)"""
650  return _IMP_bff.VectorString_reserve(self, n)
651 
652  def capacity(self):
653  r"""capacity(VectorString self) -> std::vector< std::string >::size_type"""
654  return _IMP_bff.VectorString_capacity(self)
655  __swig_destroy__ = _IMP_bff.delete_VectorString
656 
657 # Register VectorString in _IMP_bff:
658 _IMP_bff.VectorString_swigregister(VectorString)
659 class VectorDouble(object):
660  r"""Proxy of C++ std::vector< double > class."""
661 
662  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
663  __repr__ = _swig_repr
664 
665  def iterator(self):
666  r"""iterator(VectorDouble self) -> IMP_BFF_SwigPyIterator"""
667  return _IMP_bff.VectorDouble_iterator(self)
668  def __iter__(self):
669  return self.iterator()
670 
671  def __nonzero__(self):
672  r"""__nonzero__(VectorDouble self) -> bool"""
673  return _IMP_bff.VectorDouble___nonzero__(self)
674 
675  def __bool__(self):
676  r"""__bool__(VectorDouble self) -> bool"""
677  return _IMP_bff.VectorDouble___bool__(self)
678 
679  def __len__(self):
680  r"""__len__(VectorDouble self) -> std::vector< double >::size_type"""
681  return _IMP_bff.VectorDouble___len__(self)
682 
683  def __getslice__(self, i, j):
684  r"""__getslice__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::difference_type j) -> VectorDouble"""
685  return _IMP_bff.VectorDouble___getslice__(self, i, j)
686 
687  def __setslice__(self, *args):
688  r"""
689  __setslice__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)
690  __setslice__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::difference_type j, VectorDouble v)
691  """
692  return _IMP_bff.VectorDouble___setslice__(self, *args)
693 
694  def __delslice__(self, i, j):
695  r"""__delslice__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)"""
696  return _IMP_bff.VectorDouble___delslice__(self, i, j)
697 
698  def __delitem__(self, *args):
699  r"""
700  __delitem__(VectorDouble self, std::vector< double >::difference_type i)
701  __delitem__(VectorDouble self, SWIGPY_SLICEOBJECT * slice)
702  """
703  return _IMP_bff.VectorDouble___delitem__(self, *args)
704 
705  def __getitem__(self, *args):
706  r"""
707  __getitem__(VectorDouble self, SWIGPY_SLICEOBJECT * slice) -> VectorDouble
708  __getitem__(VectorDouble self, std::vector< double >::difference_type i) -> std::vector< double >::value_type const &
709  """
710  return _IMP_bff.VectorDouble___getitem__(self, *args)
711 
712  def __setitem__(self, *args):
713  r"""
714  __setitem__(VectorDouble self, SWIGPY_SLICEOBJECT * slice, VectorDouble v)
715  __setitem__(VectorDouble self, SWIGPY_SLICEOBJECT * slice)
716  __setitem__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::value_type const & x)
717  """
718  return _IMP_bff.VectorDouble___setitem__(self, *args)
719 
720  def pop(self):
721  r"""pop(VectorDouble self) -> std::vector< double >::value_type"""
722  return _IMP_bff.VectorDouble_pop(self)
723 
724  def append(self, x):
725  r"""append(VectorDouble self, std::vector< double >::value_type const & x)"""
726  return _IMP_bff.VectorDouble_append(self, x)
727 
728  def empty(self):
729  r"""empty(VectorDouble self) -> bool"""
730  return _IMP_bff.VectorDouble_empty(self)
731 
732  def size(self):
733  r"""size(VectorDouble self) -> std::vector< double >::size_type"""
734  return _IMP_bff.VectorDouble_size(self)
735 
736  def swap(self, v):
737  r"""swap(VectorDouble self, VectorDouble v)"""
738  return _IMP_bff.VectorDouble_swap(self, v)
739 
740  def begin(self):
741  r"""begin(VectorDouble self) -> std::vector< double >::iterator"""
742  return _IMP_bff.VectorDouble_begin(self)
743 
744  def end(self):
745  r"""end(VectorDouble self) -> std::vector< double >::iterator"""
746  return _IMP_bff.VectorDouble_end(self)
747 
748  def rbegin(self):
749  r"""rbegin(VectorDouble self) -> std::vector< double >::reverse_iterator"""
750  return _IMP_bff.VectorDouble_rbegin(self)
751 
752  def rend(self):
753  r"""rend(VectorDouble self) -> std::vector< double >::reverse_iterator"""
754  return _IMP_bff.VectorDouble_rend(self)
755 
756  def clear(self):
757  r"""clear(VectorDouble self)"""
758  return _IMP_bff.VectorDouble_clear(self)
759 
760  def get_allocator(self):
761  r"""get_allocator(VectorDouble self) -> std::vector< double >::allocator_type"""
762  return _IMP_bff.VectorDouble_get_allocator(self)
763 
764  def pop_back(self):
765  r"""pop_back(VectorDouble self)"""
766  return _IMP_bff.VectorDouble_pop_back(self)
767 
768  def erase(self, *args):
769  r"""
770  erase(VectorDouble self, std::vector< double >::iterator pos) -> std::vector< double >::iterator
771  erase(VectorDouble self, std::vector< double >::iterator first, std::vector< double >::iterator last) -> std::vector< double >::iterator
772  """
773  return _IMP_bff.VectorDouble_erase(self, *args)
774 
775  def __init__(self, *args):
776  r"""
777  __init__(VectorDouble self) -> VectorDouble
778  __init__(VectorDouble self, VectorDouble other) -> VectorDouble
779  __init__(VectorDouble self, std::vector< double >::size_type size) -> VectorDouble
780  __init__(VectorDouble self, std::vector< double >::size_type size, std::vector< double >::value_type const & value) -> VectorDouble
781  """
782  _IMP_bff.VectorDouble_swiginit(self, _IMP_bff.new_VectorDouble(*args))
783 
784  def push_back(self, x):
785  r"""push_back(VectorDouble self, std::vector< double >::value_type const & x)"""
786  return _IMP_bff.VectorDouble_push_back(self, x)
787 
788  def front(self):
789  r"""front(VectorDouble self) -> std::vector< double >::value_type const &"""
790  return _IMP_bff.VectorDouble_front(self)
791 
792  def back(self):
793  r"""back(VectorDouble self) -> std::vector< double >::value_type const &"""
794  return _IMP_bff.VectorDouble_back(self)
795 
796  def assign(self, n, x):
797  r"""assign(VectorDouble self, std::vector< double >::size_type n, std::vector< double >::value_type const & x)"""
798  return _IMP_bff.VectorDouble_assign(self, n, x)
799 
800  def resize(self, *args):
801  r"""
802  resize(VectorDouble self, std::vector< double >::size_type new_size)
803  resize(VectorDouble self, std::vector< double >::size_type new_size, std::vector< double >::value_type const & x)
804  """
805  return _IMP_bff.VectorDouble_resize(self, *args)
806 
807  def insert(self, *args):
808  r"""
809  insert(VectorDouble self, std::vector< double >::iterator pos, std::vector< double >::value_type const & x) -> std::vector< double >::iterator
810  insert(VectorDouble self, std::vector< double >::iterator pos, std::vector< double >::size_type n, std::vector< double >::value_type const & x)
811  """
812  return _IMP_bff.VectorDouble_insert(self, *args)
813 
814  def reserve(self, n):
815  r"""reserve(VectorDouble self, std::vector< double >::size_type n)"""
816  return _IMP_bff.VectorDouble_reserve(self, n)
817 
818  def capacity(self):
819  r"""capacity(VectorDouble self) -> std::vector< double >::size_type"""
820  return _IMP_bff.VectorDouble_capacity(self)
821  __swig_destroy__ = _IMP_bff.delete_VectorDouble
822 
823 # Register VectorDouble in _IMP_bff:
824 _IMP_bff.VectorDouble_swigregister(VectorDouble)
825 class VectorFloat(object):
826  r"""Proxy of C++ std::vector< float > class."""
827 
828  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
829  __repr__ = _swig_repr
830 
831  def iterator(self):
832  r"""iterator(VectorFloat self) -> IMP_BFF_SwigPyIterator"""
833  return _IMP_bff.VectorFloat_iterator(self)
834  def __iter__(self):
835  return self.iterator()
836 
837  def __nonzero__(self):
838  r"""__nonzero__(VectorFloat self) -> bool"""
839  return _IMP_bff.VectorFloat___nonzero__(self)
840 
841  def __bool__(self):
842  r"""__bool__(VectorFloat self) -> bool"""
843  return _IMP_bff.VectorFloat___bool__(self)
844 
845  def __len__(self):
846  r"""__len__(VectorFloat self) -> std::vector< float >::size_type"""
847  return _IMP_bff.VectorFloat___len__(self)
848 
849  def __getslice__(self, i, j):
850  r"""__getslice__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::difference_type j) -> VectorFloat"""
851  return _IMP_bff.VectorFloat___getslice__(self, i, j)
852 
853  def __setslice__(self, *args):
854  r"""
855  __setslice__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::difference_type j)
856  __setslice__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::difference_type j, VectorFloat v)
857  """
858  return _IMP_bff.VectorFloat___setslice__(self, *args)
859 
860  def __delslice__(self, i, j):
861  r"""__delslice__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::difference_type j)"""
862  return _IMP_bff.VectorFloat___delslice__(self, i, j)
863 
864  def __delitem__(self, *args):
865  r"""
866  __delitem__(VectorFloat self, std::vector< float >::difference_type i)
867  __delitem__(VectorFloat self, SWIGPY_SLICEOBJECT * slice)
868  """
869  return _IMP_bff.VectorFloat___delitem__(self, *args)
870 
871  def __getitem__(self, *args):
872  r"""
873  __getitem__(VectorFloat self, SWIGPY_SLICEOBJECT * slice) -> VectorFloat
874  __getitem__(VectorFloat self, std::vector< float >::difference_type i) -> std::vector< float >::value_type const &
875  """
876  return _IMP_bff.VectorFloat___getitem__(self, *args)
877 
878  def __setitem__(self, *args):
879  r"""
880  __setitem__(VectorFloat self, SWIGPY_SLICEOBJECT * slice, VectorFloat v)
881  __setitem__(VectorFloat self, SWIGPY_SLICEOBJECT * slice)
882  __setitem__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::value_type const & x)
883  """
884  return _IMP_bff.VectorFloat___setitem__(self, *args)
885 
886  def pop(self):
887  r"""pop(VectorFloat self) -> std::vector< float >::value_type"""
888  return _IMP_bff.VectorFloat_pop(self)
889 
890  def append(self, x):
891  r"""append(VectorFloat self, std::vector< float >::value_type const & x)"""
892  return _IMP_bff.VectorFloat_append(self, x)
893 
894  def empty(self):
895  r"""empty(VectorFloat self) -> bool"""
896  return _IMP_bff.VectorFloat_empty(self)
897 
898  def size(self):
899  r"""size(VectorFloat self) -> std::vector< float >::size_type"""
900  return _IMP_bff.VectorFloat_size(self)
901 
902  def swap(self, v):
903  r"""swap(VectorFloat self, VectorFloat v)"""
904  return _IMP_bff.VectorFloat_swap(self, v)
905 
906  def begin(self):
907  r"""begin(VectorFloat self) -> std::vector< float >::iterator"""
908  return _IMP_bff.VectorFloat_begin(self)
909 
910  def end(self):
911  r"""end(VectorFloat self) -> std::vector< float >::iterator"""
912  return _IMP_bff.VectorFloat_end(self)
913 
914  def rbegin(self):
915  r"""rbegin(VectorFloat self) -> std::vector< float >::reverse_iterator"""
916  return _IMP_bff.VectorFloat_rbegin(self)
917 
918  def rend(self):
919  r"""rend(VectorFloat self) -> std::vector< float >::reverse_iterator"""
920  return _IMP_bff.VectorFloat_rend(self)
921 
922  def clear(self):
923  r"""clear(VectorFloat self)"""
924  return _IMP_bff.VectorFloat_clear(self)
925 
926  def get_allocator(self):
927  r"""get_allocator(VectorFloat self) -> std::vector< float >::allocator_type"""
928  return _IMP_bff.VectorFloat_get_allocator(self)
929 
930  def pop_back(self):
931  r"""pop_back(VectorFloat self)"""
932  return _IMP_bff.VectorFloat_pop_back(self)
933 
934  def erase(self, *args):
935  r"""
936  erase(VectorFloat self, std::vector< float >::iterator pos) -> std::vector< float >::iterator
937  erase(VectorFloat self, std::vector< float >::iterator first, std::vector< float >::iterator last) -> std::vector< float >::iterator
938  """
939  return _IMP_bff.VectorFloat_erase(self, *args)
940 
941  def __init__(self, *args):
942  r"""
943  __init__(VectorFloat self) -> VectorFloat
944  __init__(VectorFloat self, VectorFloat other) -> VectorFloat
945  __init__(VectorFloat self, std::vector< float >::size_type size) -> VectorFloat
946  __init__(VectorFloat self, std::vector< float >::size_type size, std::vector< float >::value_type const & value) -> VectorFloat
947  """
948  _IMP_bff.VectorFloat_swiginit(self, _IMP_bff.new_VectorFloat(*args))
949 
950  def push_back(self, x):
951  r"""push_back(VectorFloat self, std::vector< float >::value_type const & x)"""
952  return _IMP_bff.VectorFloat_push_back(self, x)
953 
954  def front(self):
955  r"""front(VectorFloat self) -> std::vector< float >::value_type const &"""
956  return _IMP_bff.VectorFloat_front(self)
957 
958  def back(self):
959  r"""back(VectorFloat self) -> std::vector< float >::value_type const &"""
960  return _IMP_bff.VectorFloat_back(self)
961 
962  def assign(self, n, x):
963  r"""assign(VectorFloat self, std::vector< float >::size_type n, std::vector< float >::value_type const & x)"""
964  return _IMP_bff.VectorFloat_assign(self, n, x)
965 
966  def resize(self, *args):
967  r"""
968  resize(VectorFloat self, std::vector< float >::size_type new_size)
969  resize(VectorFloat self, std::vector< float >::size_type new_size, std::vector< float >::value_type const & x)
970  """
971  return _IMP_bff.VectorFloat_resize(self, *args)
972 
973  def insert(self, *args):
974  r"""
975  insert(VectorFloat self, std::vector< float >::iterator pos, std::vector< float >::value_type const & x) -> std::vector< float >::iterator
976  insert(VectorFloat self, std::vector< float >::iterator pos, std::vector< float >::size_type n, std::vector< float >::value_type const & x)
977  """
978  return _IMP_bff.VectorFloat_insert(self, *args)
979 
980  def reserve(self, n):
981  r"""reserve(VectorFloat self, std::vector< float >::size_type n)"""
982  return _IMP_bff.VectorFloat_reserve(self, n)
983 
984  def capacity(self):
985  r"""capacity(VectorFloat self) -> std::vector< float >::size_type"""
986  return _IMP_bff.VectorFloat_capacity(self)
987  __swig_destroy__ = _IMP_bff.delete_VectorFloat
988 
989 # Register VectorFloat in _IMP_bff:
990 _IMP_bff.VectorFloat_swigregister(VectorFloat)
991 class VectorInt(object):
992  r"""Proxy of C++ std::vector< int > class."""
993 
994  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
995  __repr__ = _swig_repr
996 
997  def iterator(self):
998  r"""iterator(VectorInt self) -> IMP_BFF_SwigPyIterator"""
999  return _IMP_bff.VectorInt_iterator(self)
1000  def __iter__(self):
1001  return self.iterator()
1002 
1003  def __nonzero__(self):
1004  r"""__nonzero__(VectorInt self) -> bool"""
1005  return _IMP_bff.VectorInt___nonzero__(self)
1006 
1007  def __bool__(self):
1008  r"""__bool__(VectorInt self) -> bool"""
1009  return _IMP_bff.VectorInt___bool__(self)
1010 
1011  def __len__(self):
1012  r"""__len__(VectorInt self) -> std::vector< int >::size_type"""
1013  return _IMP_bff.VectorInt___len__(self)
1014 
1015  def __getslice__(self, i, j):
1016  r"""__getslice__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::difference_type j) -> VectorInt"""
1017  return _IMP_bff.VectorInt___getslice__(self, i, j)
1018 
1019  def __setslice__(self, *args):
1020  r"""
1021  __setslice__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::difference_type j)
1022  __setslice__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::difference_type j, VectorInt v)
1023  """
1024  return _IMP_bff.VectorInt___setslice__(self, *args)
1025 
1026  def __delslice__(self, i, j):
1027  r"""__delslice__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::difference_type j)"""
1028  return _IMP_bff.VectorInt___delslice__(self, i, j)
1029 
1030  def __delitem__(self, *args):
1031  r"""
1032  __delitem__(VectorInt self, std::vector< int >::difference_type i)
1033  __delitem__(VectorInt self, SWIGPY_SLICEOBJECT * slice)
1034  """
1035  return _IMP_bff.VectorInt___delitem__(self, *args)
1036 
1037  def __getitem__(self, *args):
1038  r"""
1039  __getitem__(VectorInt self, SWIGPY_SLICEOBJECT * slice) -> VectorInt
1040  __getitem__(VectorInt self, std::vector< int >::difference_type i) -> std::vector< int >::value_type const &
1041  """
1042  return _IMP_bff.VectorInt___getitem__(self, *args)
1043 
1044  def __setitem__(self, *args):
1045  r"""
1046  __setitem__(VectorInt self, SWIGPY_SLICEOBJECT * slice, VectorInt v)
1047  __setitem__(VectorInt self, SWIGPY_SLICEOBJECT * slice)
1048  __setitem__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::value_type const & x)
1049  """
1050  return _IMP_bff.VectorInt___setitem__(self, *args)
1051 
1052  def pop(self):
1053  r"""pop(VectorInt self) -> std::vector< int >::value_type"""
1054  return _IMP_bff.VectorInt_pop(self)
1055 
1056  def append(self, x):
1057  r"""append(VectorInt self, std::vector< int >::value_type const & x)"""
1058  return _IMP_bff.VectorInt_append(self, x)
1059 
1060  def empty(self):
1061  r"""empty(VectorInt self) -> bool"""
1062  return _IMP_bff.VectorInt_empty(self)
1063 
1064  def size(self):
1065  r"""size(VectorInt self) -> std::vector< int >::size_type"""
1066  return _IMP_bff.VectorInt_size(self)
1067 
1068  def swap(self, v):
1069  r"""swap(VectorInt self, VectorInt v)"""
1070  return _IMP_bff.VectorInt_swap(self, v)
1071 
1072  def begin(self):
1073  r"""begin(VectorInt self) -> std::vector< int >::iterator"""
1074  return _IMP_bff.VectorInt_begin(self)
1075 
1076  def end(self):
1077  r"""end(VectorInt self) -> std::vector< int >::iterator"""
1078  return _IMP_bff.VectorInt_end(self)
1079 
1080  def rbegin(self):
1081  r"""rbegin(VectorInt self) -> std::vector< int >::reverse_iterator"""
1082  return _IMP_bff.VectorInt_rbegin(self)
1083 
1084  def rend(self):
1085  r"""rend(VectorInt self) -> std::vector< int >::reverse_iterator"""
1086  return _IMP_bff.VectorInt_rend(self)
1087 
1088  def clear(self):
1089  r"""clear(VectorInt self)"""
1090  return _IMP_bff.VectorInt_clear(self)
1091 
1092  def get_allocator(self):
1093  r"""get_allocator(VectorInt self) -> std::vector< int >::allocator_type"""
1094  return _IMP_bff.VectorInt_get_allocator(self)
1095 
1096  def pop_back(self):
1097  r"""pop_back(VectorInt self)"""
1098  return _IMP_bff.VectorInt_pop_back(self)
1099 
1100  def erase(self, *args):
1101  r"""
1102  erase(VectorInt self, std::vector< int >::iterator pos) -> std::vector< int >::iterator
1103  erase(VectorInt self, std::vector< int >::iterator first, std::vector< int >::iterator last) -> std::vector< int >::iterator
1104  """
1105  return _IMP_bff.VectorInt_erase(self, *args)
1106 
1107  def __init__(self, *args):
1108  r"""
1109  __init__(VectorInt self) -> VectorInt
1110  __init__(VectorInt self, VectorInt other) -> VectorInt
1111  __init__(VectorInt self, std::vector< int >::size_type size) -> VectorInt
1112  __init__(VectorInt self, std::vector< int >::size_type size, std::vector< int >::value_type const & value) -> VectorInt
1113  """
1114  _IMP_bff.VectorInt_swiginit(self, _IMP_bff.new_VectorInt(*args))
1115 
1116  def push_back(self, x):
1117  r"""push_back(VectorInt self, std::vector< int >::value_type const & x)"""
1118  return _IMP_bff.VectorInt_push_back(self, x)
1119 
1120  def front(self):
1121  r"""front(VectorInt self) -> std::vector< int >::value_type const &"""
1122  return _IMP_bff.VectorInt_front(self)
1123 
1124  def back(self):
1125  r"""back(VectorInt self) -> std::vector< int >::value_type const &"""
1126  return _IMP_bff.VectorInt_back(self)
1127 
1128  def assign(self, n, x):
1129  r"""assign(VectorInt self, std::vector< int >::size_type n, std::vector< int >::value_type const & x)"""
1130  return _IMP_bff.VectorInt_assign(self, n, x)
1131 
1132  def resize(self, *args):
1133  r"""
1134  resize(VectorInt self, std::vector< int >::size_type new_size)
1135  resize(VectorInt self, std::vector< int >::size_type new_size, std::vector< int >::value_type const & x)
1136  """
1137  return _IMP_bff.VectorInt_resize(self, *args)
1138 
1139  def insert(self, *args):
1140  r"""
1141  insert(VectorInt self, std::vector< int >::iterator pos, std::vector< int >::value_type const & x) -> std::vector< int >::iterator
1142  insert(VectorInt self, std::vector< int >::iterator pos, std::vector< int >::size_type n, std::vector< int >::value_type const & x)
1143  """
1144  return _IMP_bff.VectorInt_insert(self, *args)
1145 
1146  def reserve(self, n):
1147  r"""reserve(VectorInt self, std::vector< int >::size_type n)"""
1148  return _IMP_bff.VectorInt_reserve(self, n)
1149 
1150  def capacity(self):
1151  r"""capacity(VectorInt self) -> std::vector< int >::size_type"""
1152  return _IMP_bff.VectorInt_capacity(self)
1153  __swig_destroy__ = _IMP_bff.delete_VectorInt
1154 
1155 # Register VectorInt in _IMP_bff:
1156 _IMP_bff.VectorInt_swigregister(VectorInt)
1157 class VectorLong(object):
1158  r"""Proxy of C++ std::vector< long > class."""
1159 
1160  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1161  __repr__ = _swig_repr
1162 
1163  def iterator(self):
1164  r"""iterator(VectorLong self) -> IMP_BFF_SwigPyIterator"""
1165  return _IMP_bff.VectorLong_iterator(self)
1166  def __iter__(self):
1167  return self.iterator()
1168 
1169  def __nonzero__(self):
1170  r"""__nonzero__(VectorLong self) -> bool"""
1171  return _IMP_bff.VectorLong___nonzero__(self)
1172 
1173  def __bool__(self):
1174  r"""__bool__(VectorLong self) -> bool"""
1175  return _IMP_bff.VectorLong___bool__(self)
1176 
1177  def __len__(self):
1178  r"""__len__(VectorLong self) -> std::vector< long >::size_type"""
1179  return _IMP_bff.VectorLong___len__(self)
1180 
1181  def __getslice__(self, i, j):
1182  r"""__getslice__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::difference_type j) -> VectorLong"""
1183  return _IMP_bff.VectorLong___getslice__(self, i, j)
1184 
1185  def __setslice__(self, *args):
1186  r"""
1187  __setslice__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::difference_type j)
1188  __setslice__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::difference_type j, VectorLong v)
1189  """
1190  return _IMP_bff.VectorLong___setslice__(self, *args)
1191 
1192  def __delslice__(self, i, j):
1193  r"""__delslice__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::difference_type j)"""
1194  return _IMP_bff.VectorLong___delslice__(self, i, j)
1195 
1196  def __delitem__(self, *args):
1197  r"""
1198  __delitem__(VectorLong self, std::vector< long >::difference_type i)
1199  __delitem__(VectorLong self, SWIGPY_SLICEOBJECT * slice)
1200  """
1201  return _IMP_bff.VectorLong___delitem__(self, *args)
1202 
1203  def __getitem__(self, *args):
1204  r"""
1205  __getitem__(VectorLong self, SWIGPY_SLICEOBJECT * slice) -> VectorLong
1206  __getitem__(VectorLong self, std::vector< long >::difference_type i) -> std::vector< long >::value_type const &
1207  """
1208  return _IMP_bff.VectorLong___getitem__(self, *args)
1209 
1210  def __setitem__(self, *args):
1211  r"""
1212  __setitem__(VectorLong self, SWIGPY_SLICEOBJECT * slice, VectorLong v)
1213  __setitem__(VectorLong self, SWIGPY_SLICEOBJECT * slice)
1214  __setitem__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::value_type const & x)
1215  """
1216  return _IMP_bff.VectorLong___setitem__(self, *args)
1217 
1218  def pop(self):
1219  r"""pop(VectorLong self) -> std::vector< long >::value_type"""
1220  return _IMP_bff.VectorLong_pop(self)
1221 
1222  def append(self, x):
1223  r"""append(VectorLong self, std::vector< long >::value_type const & x)"""
1224  return _IMP_bff.VectorLong_append(self, x)
1225 
1226  def empty(self):
1227  r"""empty(VectorLong self) -> bool"""
1228  return _IMP_bff.VectorLong_empty(self)
1229 
1230  def size(self):
1231  r"""size(VectorLong self) -> std::vector< long >::size_type"""
1232  return _IMP_bff.VectorLong_size(self)
1233 
1234  def swap(self, v):
1235  r"""swap(VectorLong self, VectorLong v)"""
1236  return _IMP_bff.VectorLong_swap(self, v)
1237 
1238  def begin(self):
1239  r"""begin(VectorLong self) -> std::vector< long >::iterator"""
1240  return _IMP_bff.VectorLong_begin(self)
1241 
1242  def end(self):
1243  r"""end(VectorLong self) -> std::vector< long >::iterator"""
1244  return _IMP_bff.VectorLong_end(self)
1245 
1246  def rbegin(self):
1247  r"""rbegin(VectorLong self) -> std::vector< long >::reverse_iterator"""
1248  return _IMP_bff.VectorLong_rbegin(self)
1249 
1250  def rend(self):
1251  r"""rend(VectorLong self) -> std::vector< long >::reverse_iterator"""
1252  return _IMP_bff.VectorLong_rend(self)
1253 
1254  def clear(self):
1255  r"""clear(VectorLong self)"""
1256  return _IMP_bff.VectorLong_clear(self)
1257 
1258  def get_allocator(self):
1259  r"""get_allocator(VectorLong self) -> std::vector< long >::allocator_type"""
1260  return _IMP_bff.VectorLong_get_allocator(self)
1261 
1262  def pop_back(self):
1263  r"""pop_back(VectorLong self)"""
1264  return _IMP_bff.VectorLong_pop_back(self)
1265 
1266  def erase(self, *args):
1267  r"""
1268  erase(VectorLong self, std::vector< long >::iterator pos) -> std::vector< long >::iterator
1269  erase(VectorLong self, std::vector< long >::iterator first, std::vector< long >::iterator last) -> std::vector< long >::iterator
1270  """
1271  return _IMP_bff.VectorLong_erase(self, *args)
1272 
1273  def __init__(self, *args):
1274  r"""
1275  __init__(VectorLong self) -> VectorLong
1276  __init__(VectorLong self, VectorLong other) -> VectorLong
1277  __init__(VectorLong self, std::vector< long >::size_type size) -> VectorLong
1278  __init__(VectorLong self, std::vector< long >::size_type size, std::vector< long >::value_type const & value) -> VectorLong
1279  """
1280  _IMP_bff.VectorLong_swiginit(self, _IMP_bff.new_VectorLong(*args))
1281 
1282  def push_back(self, x):
1283  r"""push_back(VectorLong self, std::vector< long >::value_type const & x)"""
1284  return _IMP_bff.VectorLong_push_back(self, x)
1285 
1286  def front(self):
1287  r"""front(VectorLong self) -> std::vector< long >::value_type const &"""
1288  return _IMP_bff.VectorLong_front(self)
1289 
1290  def back(self):
1291  r"""back(VectorLong self) -> std::vector< long >::value_type const &"""
1292  return _IMP_bff.VectorLong_back(self)
1293 
1294  def assign(self, n, x):
1295  r"""assign(VectorLong self, std::vector< long >::size_type n, std::vector< long >::value_type const & x)"""
1296  return _IMP_bff.VectorLong_assign(self, n, x)
1297 
1298  def resize(self, *args):
1299  r"""
1300  resize(VectorLong self, std::vector< long >::size_type new_size)
1301  resize(VectorLong self, std::vector< long >::size_type new_size, std::vector< long >::value_type const & x)
1302  """
1303  return _IMP_bff.VectorLong_resize(self, *args)
1304 
1305  def insert(self, *args):
1306  r"""
1307  insert(VectorLong self, std::vector< long >::iterator pos, std::vector< long >::value_type const & x) -> std::vector< long >::iterator
1308  insert(VectorLong self, std::vector< long >::iterator pos, std::vector< long >::size_type n, std::vector< long >::value_type const & x)
1309  """
1310  return _IMP_bff.VectorLong_insert(self, *args)
1311 
1312  def reserve(self, n):
1313  r"""reserve(VectorLong self, std::vector< long >::size_type n)"""
1314  return _IMP_bff.VectorLong_reserve(self, n)
1315 
1316  def capacity(self):
1317  r"""capacity(VectorLong self) -> std::vector< long >::size_type"""
1318  return _IMP_bff.VectorLong_capacity(self)
1319  __swig_destroy__ = _IMP_bff.delete_VectorLong
1320 
1321 # Register VectorLong in _IMP_bff:
1322 _IMP_bff.VectorLong_swigregister(VectorLong)
1323 
1324 PathMapTileEdges=list
1325 _plural_types.append("PathMapTileEdges")
1326 _value_types.append("PathMapTileEdge")
1327 
1328 
1329 _object_types.append("PathMap")
1330 
1331 
1332 def _object_cast_to_PathMap(o):
1333  r"""_object_cast_to_PathMap(Object o) -> PathMap"""
1334  return _IMP_bff._object_cast_to_PathMap(o)
1335 class PathMapHeader(object):
1336  r"""Proxy of C++ IMP::bff::PathMapHeader class."""
1337 
1338  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1339  __repr__ = _swig_repr
1340  __swig_destroy__ = _IMP_bff.delete_PathMapHeader
1341 
1342  def __init__(self, *args, **kwargs):
1343  r"""__init__(PathMapHeader self, double max_path_length=10.0, double grid_spacing=1.0, double neighbor_radius=2, double obstacle_threshold=std::numeric_limits< double >::epsilon()) -> PathMapHeader"""
1344  _IMP_bff.PathMapHeader_swiginit(self, _IMP_bff.new_PathMapHeader(*args, **kwargs))
1345 
1346  def update_map_dimensions(self, nx=-1, ny=-1, nz=-1):
1347  r"""update_map_dimensions(PathMapHeader self, int nx=-1, int ny=-1, int nz=-1)"""
1348  return _IMP_bff.PathMapHeader_update_map_dimensions(self, nx, ny, nz)
1349 
1350  def set_path_origin(self, v):
1351  r"""set_path_origin(PathMapHeader self, Vector3D v)"""
1352  return _IMP_bff.PathMapHeader_set_path_origin(self, v)
1353 
1354  def get_path_origin(self):
1355  r"""get_path_origin(PathMapHeader self) -> Vector3D"""
1356  return _IMP_bff.PathMapHeader_get_path_origin(self)
1357 
1358  def get_max_path_length(self):
1359  r"""get_max_path_length(PathMapHeader self) -> double"""
1360  return _IMP_bff.PathMapHeader_get_max_path_length(self)
1361 
1362  def get_simulation_grid_resolution(self):
1363  r"""get_simulation_grid_resolution(PathMapHeader self) -> double"""
1364  return _IMP_bff.PathMapHeader_get_simulation_grid_resolution(self)
1365 
1366  def set_obstacle_threshold(self, obstacle_threshold):
1367  r"""set_obstacle_threshold(PathMapHeader self, double obstacle_threshold)"""
1368  return _IMP_bff.PathMapHeader_set_obstacle_threshold(self, obstacle_threshold)
1369 
1370  def get_obstacle_threshold(self):
1371  r"""get_obstacle_threshold(PathMapHeader self) -> double"""
1372  return _IMP_bff.PathMapHeader_get_obstacle_threshold(self)
1373 
1374  def set_neighbor_radius(self, neighbor_radius):
1375  r"""set_neighbor_radius(PathMapHeader self, double neighbor_radius)"""
1376  return _IMP_bff.PathMapHeader_set_neighbor_radius(self, neighbor_radius)
1377 
1378  def get_neighbor_radius(self):
1379  r"""get_neighbor_radius(PathMapHeader self) -> double"""
1380  return _IMP_bff.PathMapHeader_get_neighbor_radius(self)
1381 
1382  def get_neighbor_box_size(self):
1383  r"""get_neighbor_box_size(PathMapHeader self) -> int"""
1384  return _IMP_bff.PathMapHeader_get_neighbor_box_size(self)
1385 
1386  def get_density_header(self):
1387  r"""get_density_header(PathMapHeader self) -> DensityHeader"""
1388  return _IMP_bff.PathMapHeader_get_density_header(self)
1389 
1390  def get_density_header_writable(self):
1391  r"""get_density_header_writable(PathMapHeader self) -> DensityHeader"""
1392  return _IMP_bff.PathMapHeader_get_density_header_writable(self)
1393 
1394  def get_origin(self):
1395  r"""get_origin(PathMapHeader self) -> Vector3D"""
1396  return _IMP_bff.PathMapHeader_get_origin(self)
1397 
1398  def get_grid_edge_length(self):
1399  r"""get_grid_edge_length(PathMapHeader self) -> double"""
1400  return _IMP_bff.PathMapHeader_get_grid_edge_length(self)
1401 
1402  def set_origin(self, x, y, z):
1403  r"""set_origin(PathMapHeader self, float x, float y, float z)"""
1404  return _IMP_bff.PathMapHeader_set_origin(self, x, y, z)
1405 
1406  def show(self, *args, **kwargs):
1407  r"""show(PathMapHeader self, _ostream out=std::cout)"""
1408  return _IMP_bff.PathMapHeader_show(self, *args, **kwargs)
1409 
1410 # Register PathMapHeader in _IMP_bff:
1411 _IMP_bff.PathMapHeader_swigregister(PathMapHeader)
1412 class PathMap(IMP.em.SampledDensityMap):
1413  r"""Proxy of C++ IMP::bff::PathMap class."""
1414 
1415  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1416 
1417  def update_tiles(self, *args, **kwargs):
1418  r"""update_tiles(PathMap self, float obstacle_threshold=-1.0, bool binarize=True, float obstacle_penalty=TILE_PENALTY_DEFAULT, bool reset_tile_edges=True)"""
1419  return _IMP_bff.PathMap_update_tiles(self, *args, **kwargs)
1420 
1421  def resize(self, nvox):
1422  r"""resize(PathMap self, unsigned int nvox)"""
1423  return _IMP_bff.PathMap_resize(self, nvox)
1424 
1425  def set_data(self, *args, **kwargs):
1426  r"""set_data(PathMap self, double * input, float obstacle_threshold=-1, bool binarize=True, float obstacle_penalty=TILE_PENALTY_DEFAULT)"""
1427  return _IMP_bff.PathMap_set_data(self, *args, **kwargs)
1428 
1429  def get_neighbor_idx_offsets(self, neighbor_radius=-1):
1430  r"""get_neighbor_idx_offsets(PathMap self, double neighbor_radius=-1) -> VectorInt"""
1431  return _IMP_bff.PathMap_get_neighbor_idx_offsets(self, neighbor_radius)
1432 
1433  def get_dim_index_by_voxel(self, index, dim):
1434  r"""get_dim_index_by_voxel(PathMap self, long index, int dim) -> int"""
1435  return _IMP_bff.PathMap_get_dim_index_by_voxel(self, index, dim)
1436 
1437  def get_path_map_header(self):
1438  h = _IMP_bff.DensityMap_get_path_map_header(self)
1439  h._owner = self
1440  return h
1441 
1442 
1443 
1444  def get_path_map_header_writable(self):
1445  h = _IMP_bff.PathMap_get_path_map_header_writable(self)
1446  h._owner = self
1447  return h
1448 
1449 
1450 
1451  def set_path_map_header(self, path_map_header, resolution=-1.0):
1452  r"""set_path_map_header(PathMap self, PathMapHeader path_map_header, float resolution=-1.0)"""
1453  return _IMP_bff.PathMap_set_path_map_header(self, path_map_header, resolution)
1454 
1455  def get_tile_values(self, *args, **kwargs):
1456  r"""get_tile_values(PathMap self, int value_type=PM_TILE_COST, PairFloatFloat bounds=std::pair< float,float >( {std::numeric_limits<float>::min(), std::numeric_limits<float>::max()}), std::string const & feature_name="")"""
1457  return _IMP_bff.PathMap_get_tile_values(self, *args, **kwargs)
1458 
1459  def get_tiles(self):
1460  r"""get_tiles(PathMap self) -> VectorPathMapTile"""
1461  return _IMP_bff.PathMap_get_tiles(self)
1462 
1463  def fill_sphere(self, r0, radius, value, inverse=True):
1464  r"""fill_sphere(PathMap self, Vector3D r0, double radius, double value, bool inverse=True)"""
1465  return _IMP_bff.PathMap_fill_sphere(self, r0, radius, value, inverse)
1466 
1467  def find_path(self, path_begin_idx, path_end_idx=-1, heuristic_mode=0):
1468  r"""find_path(PathMap self, long path_begin_idx, long path_end_idx=-1, int heuristic_mode=0)"""
1469  return _IMP_bff.PathMap_find_path(self, path_begin_idx, path_end_idx, heuristic_mode)
1470 
1471  def find_path_dijkstra(self, path_begin_idx, path_end_idx=-1):
1472  r"""find_path_dijkstra(PathMap self, long path_begin_idx, long path_end_idx=-1)"""
1473  return _IMP_bff.PathMap_find_path_dijkstra(self, path_begin_idx, path_end_idx)
1474 
1475  def find_path_astar(self, path_begin_idx, path_end_idx=-1):
1476  r"""find_path_astar(PathMap self, long path_begin_idx, long path_end_idx=-1)"""
1477  return _IMP_bff.PathMap_find_path_astar(self, path_begin_idx, path_end_idx)
1478 
1479  def get_xyz_density(self):
1480  r"""get_xyz_density(PathMap self)"""
1481  return _IMP_bff.PathMap_get_xyz_density(self)
1482 
1483  def sample_obstacles(self, extra_radius=0.0):
1484  r"""sample_obstacles(PathMap self, double extra_radius=0.0)"""
1485  return _IMP_bff.PathMap_sample_obstacles(self, extra_radius)
1486 
1487  def __init__(self, *args, **kwargs):
1488  r"""__init__(PathMap self, PathMapHeader header, std::string name="PathMap%1%", IMP::em::KernelType kt=BINARIZED_SPHERE, float resolution=-1.0) -> PathMap"""
1489  _IMP_bff.PathMap_swiginit(self, _IMP_bff.new_PathMap(*args, **kwargs))
1490 
1491  def __str__(self):
1492  r"""__str__(PathMap self) -> std::string"""
1493  return _IMP_bff.PathMap___str__(self)
1494 
1495  def __repr__(self):
1496  r"""__repr__(PathMap self) -> std::string"""
1497  return _IMP_bff.PathMap___repr__(self)
1498 
1499  @staticmethod
1500  def get_from(o):
1501  return _object_cast_to_PathMap(o)
1502 
1503  __swig_destroy__ = _IMP_bff.delete_PathMap
1504 
1505 # Register PathMap in _IMP_bff:
1506 _IMP_bff.PathMap_swigregister(PathMap)
1507 
1508 def write_path_map(*args, **kwargs):
1509  r"""write_path_map(PathMap m, std::string filename, int value_type, PairFloatFloat bounds=std::pair< float,float >( std::numeric_limits<float>::min(), std::numeric_limits<float>::max() ), std::string const & feature_name="")"""
1510  return _IMP_bff.write_path_map(*args, **kwargs)
1511 PM_TILE_PENALTY = _IMP_bff.PM_TILE_PENALTY
1512 
1513 PM_TILE_COST = _IMP_bff.PM_TILE_COST
1514 
1515 PM_TILE_DENSITY = _IMP_bff.PM_TILE_DENSITY
1516 
1517 PM_TILE_COST_DENSITY = _IMP_bff.PM_TILE_COST_DENSITY
1518 
1519 PM_TILE_PATH_LENGTH = _IMP_bff.PM_TILE_PATH_LENGTH
1520 
1521 PM_TILE_PATH_LENGTH_DENSITY = _IMP_bff.PM_TILE_PATH_LENGTH_DENSITY
1522 
1523 PM_TILE_FEATURE = _IMP_bff.PM_TILE_FEATURE
1524 
1525 PM_TILE_ACCESSIBLE_DENSITY = _IMP_bff.PM_TILE_ACCESSIBLE_DENSITY
1526 
1527 PM_TILE_ACCESSIBLE_FEATURE = _IMP_bff.PM_TILE_ACCESSIBLE_FEATURE
1528 
1529 class PathMapTile(object):
1530  r"""Proxy of C++ IMP::bff::PathMapTile class."""
1531 
1532  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1533  __repr__ = _swig_repr
1534  density = property(_IMP_bff.PathMapTile_density_get, _IMP_bff.PathMapTile_density_set, doc=r"""density : float""")
1535 
1536  def __init__(self, index=-1, visit_penalty=0.0, tile_density=1.0):
1537  r"""__init__(PathMapTile self, long index=-1, float visit_penalty=0.0, float tile_density=1.0) -> PathMapTile"""
1538  _IMP_bff.PathMapTile_swiginit(self, _IMP_bff.new_PathMapTile(index, visit_penalty, tile_density))
1539 
1540  def backtrack_to_path(self):
1541  r"""backtrack_to_path(PathMapTile self) -> VectorLong"""
1542  return _IMP_bff.PathMapTile_backtrack_to_path(self)
1543 
1544  def get_value(self, *args, **kwargs):
1545  r"""get_value(PathMapTile self, int value_type, PairFloatFloat bounds=std::pair< float,float >( {std::numeric_limits<float>::min(), std::numeric_limits<float>::max()}), std::string const & feature_name="", float grid_spacing=1.0) -> float"""
1546  return _IMP_bff.PathMapTile_get_value(self, *args, **kwargs)
1547 
1548  def set_value(self, *args, **kwargs):
1549  r"""set_value(PathMapTile self, int value_type, float value, std::string const & name="")"""
1550  return _IMP_bff.PathMapTile_set_value(self, *args, **kwargs)
1551  __swig_destroy__ = _IMP_bff.delete_PathMapTile
1552 
1553 # Register PathMapTile in _IMP_bff:
1554 _IMP_bff.PathMapTile_swigregister(PathMapTile)
1555 cvar = _IMP_bff.cvar
1556 TILE_VISITED_DEFAULT = cvar.TILE_VISITED_DEFAULT
1557 TILE_PENALTY_DEFAULT = cvar.TILE_PENALTY_DEFAULT
1558 TILE_COST_DEFAULT = cvar.TILE_COST_DEFAULT
1559 TILE_EDGE_COST_DEFAULT = cvar.TILE_EDGE_COST_DEFAULT
1560 TILE_PENALTY_THRESHOLD = cvar.TILE_PENALTY_THRESHOLD
1561 TILE_OBSTACLE_THRESHOLD = cvar.TILE_OBSTACLE_THRESHOLD
1562 TILE_OBSTACLE_PENALTY = cvar.TILE_OBSTACLE_PENALTY
1563 
1564 class PathMapTileEdge(IMP._Value):
1565  r"""Proxy of C++ IMP::bff::PathMapTileEdge class."""
1566 
1567  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1568 
1569  def get_length(self):
1570  r"""get_length(PathMapTileEdge self) -> float"""
1571  return _IMP_bff.PathMapTileEdge_get_length(self)
1572 
1573  def __init__(self, *args, **kwargs):
1574  r"""__init__(PathMapTileEdge self, int edge_target=-1, float edge_cost=std::numeric_limits< float >::max()) -> PathMapTileEdge"""
1575  _IMP_bff.PathMapTileEdge_swiginit(self, _IMP_bff.new_PathMapTileEdge(*args, **kwargs))
1576 
1577  def show(self, *args, **kwargs):
1578  r"""show(PathMapTileEdge self, _ostream out=std::cout)"""
1579  return _IMP_bff.PathMapTileEdge_show(self, *args, **kwargs)
1580 
1581  def __str__(self):
1582  r"""__str__(PathMapTileEdge self) -> std::string"""
1583  return _IMP_bff.PathMapTileEdge___str__(self)
1584 
1585  def __repr__(self):
1586  r"""__repr__(PathMapTileEdge self) -> std::string"""
1587  return _IMP_bff.PathMapTileEdge___repr__(self)
1588  __swig_destroy__ = _IMP_bff.delete_PathMapTileEdge
1589 
1590 # Register PathMapTileEdge in _IMP_bff:
1591 _IMP_bff.PathMapTileEdge_swigregister(PathMapTileEdge)
1592 class VectorPathMapTile(object):
1593  r"""Proxy of C++ std::vector< IMP::bff::PathMapTile > class."""
1594 
1595  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1596  __repr__ = _swig_repr
1597 
1598  def iterator(self):
1599  r"""iterator(VectorPathMapTile self) -> IMP_BFF_SwigPyIterator"""
1600  return _IMP_bff.VectorPathMapTile_iterator(self)
1601  def __iter__(self):
1602  return self.iterator()
1603 
1604  def __nonzero__(self):
1605  r"""__nonzero__(VectorPathMapTile self) -> bool"""
1606  return _IMP_bff.VectorPathMapTile___nonzero__(self)
1607 
1608  def __bool__(self):
1609  r"""__bool__(VectorPathMapTile self) -> bool"""
1610  return _IMP_bff.VectorPathMapTile___bool__(self)
1611 
1612  def __len__(self):
1613  r"""__len__(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::size_type"""
1614  return _IMP_bff.VectorPathMapTile___len__(self)
1615 
1616  def __getslice__(self, i, j):
1617  r"""__getslice__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, std::vector< IMP::bff::PathMapTile >::difference_type j) -> VectorPathMapTile"""
1618  return _IMP_bff.VectorPathMapTile___getslice__(self, i, j)
1619 
1620  def __setslice__(self, *args):
1621  r"""
1622  __setslice__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, std::vector< IMP::bff::PathMapTile >::difference_type j)
1623  __setslice__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, std::vector< IMP::bff::PathMapTile >::difference_type j, VectorPathMapTile v)
1624  """
1625  return _IMP_bff.VectorPathMapTile___setslice__(self, *args)
1626 
1627  def __delslice__(self, i, j):
1628  r"""__delslice__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, std::vector< IMP::bff::PathMapTile >::difference_type j)"""
1629  return _IMP_bff.VectorPathMapTile___delslice__(self, i, j)
1630 
1631  def __delitem__(self, *args):
1632  r"""
1633  __delitem__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i)
1634  __delitem__(VectorPathMapTile self, SWIGPY_SLICEOBJECT * slice)
1635  """
1636  return _IMP_bff.VectorPathMapTile___delitem__(self, *args)
1637 
1638  def __getitem__(self, *args):
1639  r"""
1640  __getitem__(VectorPathMapTile self, SWIGPY_SLICEOBJECT * slice) -> VectorPathMapTile
1641  __getitem__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i) -> PathMapTile
1642  """
1643  return _IMP_bff.VectorPathMapTile___getitem__(self, *args)
1644 
1645  def __setitem__(self, *args):
1646  r"""
1647  __setitem__(VectorPathMapTile self, SWIGPY_SLICEOBJECT * slice, VectorPathMapTile v)
1648  __setitem__(VectorPathMapTile self, SWIGPY_SLICEOBJECT * slice)
1649  __setitem__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, PathMapTile x)
1650  """
1651  return _IMP_bff.VectorPathMapTile___setitem__(self, *args)
1652 
1653  def pop(self):
1654  r"""pop(VectorPathMapTile self) -> PathMapTile"""
1655  return _IMP_bff.VectorPathMapTile_pop(self)
1656 
1657  def append(self, x):
1658  r"""append(VectorPathMapTile self, PathMapTile x)"""
1659  return _IMP_bff.VectorPathMapTile_append(self, x)
1660 
1661  def empty(self):
1662  r"""empty(VectorPathMapTile self) -> bool"""
1663  return _IMP_bff.VectorPathMapTile_empty(self)
1664 
1665  def size(self):
1666  r"""size(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::size_type"""
1667  return _IMP_bff.VectorPathMapTile_size(self)
1668 
1669  def swap(self, v):
1670  r"""swap(VectorPathMapTile self, VectorPathMapTile v)"""
1671  return _IMP_bff.VectorPathMapTile_swap(self, v)
1672 
1673  def begin(self):
1674  r"""begin(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::iterator"""
1675  return _IMP_bff.VectorPathMapTile_begin(self)
1676 
1677  def end(self):
1678  r"""end(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::iterator"""
1679  return _IMP_bff.VectorPathMapTile_end(self)
1680 
1681  def rbegin(self):
1682  r"""rbegin(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::reverse_iterator"""
1683  return _IMP_bff.VectorPathMapTile_rbegin(self)
1684 
1685  def rend(self):
1686  r"""rend(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::reverse_iterator"""
1687  return _IMP_bff.VectorPathMapTile_rend(self)
1688 
1689  def clear(self):
1690  r"""clear(VectorPathMapTile self)"""
1691  return _IMP_bff.VectorPathMapTile_clear(self)
1692 
1693  def get_allocator(self):
1694  r"""get_allocator(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::allocator_type"""
1695  return _IMP_bff.VectorPathMapTile_get_allocator(self)
1696 
1697  def pop_back(self):
1698  r"""pop_back(VectorPathMapTile self)"""
1699  return _IMP_bff.VectorPathMapTile_pop_back(self)
1700 
1701  def erase(self, *args):
1702  r"""
1703  erase(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::iterator pos) -> std::vector< IMP::bff::PathMapTile >::iterator
1704  erase(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::iterator first, std::vector< IMP::bff::PathMapTile >::iterator last) -> std::vector< IMP::bff::PathMapTile >::iterator
1705  """
1706  return _IMP_bff.VectorPathMapTile_erase(self, *args)
1707 
1708  def __init__(self, *args):
1709  r"""
1710  __init__(VectorPathMapTile self) -> VectorPathMapTile
1711  __init__(VectorPathMapTile self, VectorPathMapTile other) -> VectorPathMapTile
1712  __init__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type size) -> VectorPathMapTile
1713  __init__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type size, PathMapTile value) -> VectorPathMapTile
1714  """
1715  _IMP_bff.VectorPathMapTile_swiginit(self, _IMP_bff.new_VectorPathMapTile(*args))
1716 
1717  def push_back(self, x):
1718  r"""push_back(VectorPathMapTile self, PathMapTile x)"""
1719  return _IMP_bff.VectorPathMapTile_push_back(self, x)
1720 
1721  def front(self):
1722  r"""front(VectorPathMapTile self) -> PathMapTile"""
1723  return _IMP_bff.VectorPathMapTile_front(self)
1724 
1725  def back(self):
1726  r"""back(VectorPathMapTile self) -> PathMapTile"""
1727  return _IMP_bff.VectorPathMapTile_back(self)
1728 
1729  def assign(self, n, x):
1730  r"""assign(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type n, PathMapTile x)"""
1731  return _IMP_bff.VectorPathMapTile_assign(self, n, x)
1732 
1733  def resize(self, *args):
1734  r"""
1735  resize(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type new_size)
1736  resize(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type new_size, PathMapTile x)
1737  """
1738  return _IMP_bff.VectorPathMapTile_resize(self, *args)
1739 
1740  def insert(self, *args):
1741  r"""
1742  insert(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::iterator pos, PathMapTile x) -> std::vector< IMP::bff::PathMapTile >::iterator
1743  insert(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::iterator pos, std::vector< IMP::bff::PathMapTile >::size_type n, PathMapTile x)
1744  """
1745  return _IMP_bff.VectorPathMapTile_insert(self, *args)
1746 
1747  def reserve(self, n):
1748  r"""reserve(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type n)"""
1749  return _IMP_bff.VectorPathMapTile_reserve(self, n)
1750 
1751  def capacity(self):
1752  r"""capacity(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::size_type"""
1753  return _IMP_bff.VectorPathMapTile_capacity(self)
1754  __swig_destroy__ = _IMP_bff.delete_VectorPathMapTile
1755 
1756 # Register VectorPathMapTile in _IMP_bff:
1757 _IMP_bff.VectorPathMapTile_swigregister(VectorPathMapTile)
1758 class VectorPathMapTileEdge(object):
1759  r"""Proxy of C++ std::vector< IMP::bff::PathMapTileEdge > class."""
1760 
1761  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1762  __repr__ = _swig_repr
1763 
1764  def iterator(self):
1765  r"""iterator(VectorPathMapTileEdge self) -> IMP_BFF_SwigPyIterator"""
1766  return _IMP_bff.VectorPathMapTileEdge_iterator(self)
1767  def __iter__(self):
1768  return self.iterator()
1769 
1770  def __nonzero__(self):
1771  r"""__nonzero__(VectorPathMapTileEdge self) -> bool"""
1772  return _IMP_bff.VectorPathMapTileEdge___nonzero__(self)
1773 
1774  def __bool__(self):
1775  r"""__bool__(VectorPathMapTileEdge self) -> bool"""
1776  return _IMP_bff.VectorPathMapTileEdge___bool__(self)
1777 
1778  def __len__(self):
1779  r"""__len__(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::size_type"""
1780  return _IMP_bff.VectorPathMapTileEdge___len__(self)
1781 
1782  def __getslice__(self, i, j):
1783  r"""__getslice__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, std::vector< IMP::bff::PathMapTileEdge >::difference_type j) -> VectorPathMapTileEdge"""
1784  return _IMP_bff.VectorPathMapTileEdge___getslice__(self, i, j)
1785 
1786  def __setslice__(self, *args):
1787  r"""
1788  __setslice__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, std::vector< IMP::bff::PathMapTileEdge >::difference_type j)
1789  __setslice__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, std::vector< IMP::bff::PathMapTileEdge >::difference_type j, VectorPathMapTileEdge v)
1790  """
1791  return _IMP_bff.VectorPathMapTileEdge___setslice__(self, *args)
1792 
1793  def __delslice__(self, i, j):
1794  r"""__delslice__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, std::vector< IMP::bff::PathMapTileEdge >::difference_type j)"""
1795  return _IMP_bff.VectorPathMapTileEdge___delslice__(self, i, j)
1796 
1797  def __delitem__(self, *args):
1798  r"""
1799  __delitem__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i)
1800  __delitem__(VectorPathMapTileEdge self, SWIGPY_SLICEOBJECT * slice)
1801  """
1802  return _IMP_bff.VectorPathMapTileEdge___delitem__(self, *args)
1803 
1804  def __getitem__(self, *args):
1805  r"""
1806  __getitem__(VectorPathMapTileEdge self, SWIGPY_SLICEOBJECT * slice) -> VectorPathMapTileEdge
1807  __getitem__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i) -> PathMapTileEdge
1808  """
1809  return _IMP_bff.VectorPathMapTileEdge___getitem__(self, *args)
1810 
1811  def __setitem__(self, *args):
1812  r"""
1813  __setitem__(VectorPathMapTileEdge self, SWIGPY_SLICEOBJECT * slice, VectorPathMapTileEdge v)
1814  __setitem__(VectorPathMapTileEdge self, SWIGPY_SLICEOBJECT * slice)
1815  __setitem__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, PathMapTileEdge x)
1816  """
1817  return _IMP_bff.VectorPathMapTileEdge___setitem__(self, *args)
1818 
1819  def pop(self):
1820  r"""pop(VectorPathMapTileEdge self) -> PathMapTileEdge"""
1821  return _IMP_bff.VectorPathMapTileEdge_pop(self)
1822 
1823  def append(self, x):
1824  r"""append(VectorPathMapTileEdge self, PathMapTileEdge x)"""
1825  return _IMP_bff.VectorPathMapTileEdge_append(self, x)
1826 
1827  def empty(self):
1828  r"""empty(VectorPathMapTileEdge self) -> bool"""
1829  return _IMP_bff.VectorPathMapTileEdge_empty(self)
1830 
1831  def size(self):
1832  r"""size(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::size_type"""
1833  return _IMP_bff.VectorPathMapTileEdge_size(self)
1834 
1835  def swap(self, v):
1836  r"""swap(VectorPathMapTileEdge self, VectorPathMapTileEdge v)"""
1837  return _IMP_bff.VectorPathMapTileEdge_swap(self, v)
1838 
1839  def begin(self):
1840  r"""begin(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::iterator"""
1841  return _IMP_bff.VectorPathMapTileEdge_begin(self)
1842 
1843  def end(self):
1844  r"""end(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::iterator"""
1845  return _IMP_bff.VectorPathMapTileEdge_end(self)
1846 
1847  def rbegin(self):
1848  r"""rbegin(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::reverse_iterator"""
1849  return _IMP_bff.VectorPathMapTileEdge_rbegin(self)
1850 
1851  def rend(self):
1852  r"""rend(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::reverse_iterator"""
1853  return _IMP_bff.VectorPathMapTileEdge_rend(self)
1854 
1855  def clear(self):
1856  r"""clear(VectorPathMapTileEdge self)"""
1857  return _IMP_bff.VectorPathMapTileEdge_clear(self)
1858 
1859  def get_allocator(self):
1860  r"""get_allocator(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::allocator_type"""
1861  return _IMP_bff.VectorPathMapTileEdge_get_allocator(self)
1862 
1863  def pop_back(self):
1864  r"""pop_back(VectorPathMapTileEdge self)"""
1865  return _IMP_bff.VectorPathMapTileEdge_pop_back(self)
1866 
1867  def erase(self, *args):
1868  r"""
1869  erase(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::iterator pos) -> std::vector< IMP::bff::PathMapTileEdge >::iterator
1870  erase(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::iterator first, std::vector< IMP::bff::PathMapTileEdge >::iterator last) -> std::vector< IMP::bff::PathMapTileEdge >::iterator
1871  """
1872  return _IMP_bff.VectorPathMapTileEdge_erase(self, *args)
1873 
1874  def __init__(self, *args):
1875  r"""
1876  __init__(VectorPathMapTileEdge self) -> VectorPathMapTileEdge
1877  __init__(VectorPathMapTileEdge self, VectorPathMapTileEdge other) -> VectorPathMapTileEdge
1878  __init__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type size) -> VectorPathMapTileEdge
1879  __init__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type size, PathMapTileEdge value) -> VectorPathMapTileEdge
1880  """
1881  _IMP_bff.VectorPathMapTileEdge_swiginit(self, _IMP_bff.new_VectorPathMapTileEdge(*args))
1882 
1883  def push_back(self, x):
1884  r"""push_back(VectorPathMapTileEdge self, PathMapTileEdge x)"""
1885  return _IMP_bff.VectorPathMapTileEdge_push_back(self, x)
1886 
1887  def front(self):
1888  r"""front(VectorPathMapTileEdge self) -> PathMapTileEdge"""
1889  return _IMP_bff.VectorPathMapTileEdge_front(self)
1890 
1891  def back(self):
1892  r"""back(VectorPathMapTileEdge self) -> PathMapTileEdge"""
1893  return _IMP_bff.VectorPathMapTileEdge_back(self)
1894 
1895  def assign(self, n, x):
1896  r"""assign(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type n, PathMapTileEdge x)"""
1897  return _IMP_bff.VectorPathMapTileEdge_assign(self, n, x)
1898 
1899  def resize(self, *args):
1900  r"""
1901  resize(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type new_size)
1902  resize(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type new_size, PathMapTileEdge x)
1903  """
1904  return _IMP_bff.VectorPathMapTileEdge_resize(self, *args)
1905 
1906  def insert(self, *args):
1907  r"""
1908  insert(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::iterator pos, PathMapTileEdge x) -> std::vector< IMP::bff::PathMapTileEdge >::iterator
1909  insert(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::iterator pos, std::vector< IMP::bff::PathMapTileEdge >::size_type n, PathMapTileEdge x)
1910  """
1911  return _IMP_bff.VectorPathMapTileEdge_insert(self, *args)
1912 
1913  def reserve(self, n):
1914  r"""reserve(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type n)"""
1915  return _IMP_bff.VectorPathMapTileEdge_reserve(self, n)
1916 
1917  def capacity(self):
1918  r"""capacity(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::size_type"""
1919  return _IMP_bff.VectorPathMapTileEdge_capacity(self)
1920  __swig_destroy__ = _IMP_bff.delete_VectorPathMapTileEdge
1921 
1922 # Register VectorPathMapTileEdge in _IMP_bff:
1923 _IMP_bff.VectorPathMapTileEdge_swigregister(VectorPathMapTileEdge)
1924 
1925 def AVs(l=[]):
1926  return [AV(x) for x in l]
1927 _plural_types.append("AVs")
1928 
1929 
1930 _value_types.append("AV")
1931 
1932 
1933 AVPairDistanceMeasurements=list
1934 _plural_types.append("AVPairDistanceMeasurements")
1935 _value_types.append("AVPairDistanceMeasurement")
1936 
1937 
1938 _object_types.append("AVNetworkRestraint")
1939 
1940 
1941 def _object_cast_to_AVNetworkRestraint(o):
1942  r"""_object_cast_to_AVNetworkRestraint(Object o) -> AVNetworkRestraint"""
1943  return _IMP_bff._object_cast_to_AVNetworkRestraint(o)
1944 class MapStringAVPairDistanceMeasurement(object):
1945  r"""Proxy of C++ std::map< std::string,IMP::bff::AVPairDistanceMeasurement > class."""
1946 
1947  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1948  __repr__ = _swig_repr
1949 
1950  def iterator(self):
1951  r"""iterator(MapStringAVPairDistanceMeasurement self) -> IMP_BFF_SwigPyIterator"""
1952  return _IMP_bff.MapStringAVPairDistanceMeasurement_iterator(self)
1953  def __iter__(self):
1954  return self.iterator()
1955 
1956  def __nonzero__(self):
1957  r"""__nonzero__(MapStringAVPairDistanceMeasurement self) -> bool"""
1958  return _IMP_bff.MapStringAVPairDistanceMeasurement___nonzero__(self)
1959 
1960  def __bool__(self):
1961  r"""__bool__(MapStringAVPairDistanceMeasurement self) -> bool"""
1962  return _IMP_bff.MapStringAVPairDistanceMeasurement___bool__(self)
1963 
1964  def __len__(self):
1965  r"""__len__(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::size_type"""
1966  return _IMP_bff.MapStringAVPairDistanceMeasurement___len__(self)
1967  def __iter__(self):
1968  return self.key_iterator()
1969  def iterkeys(self):
1970  return self.key_iterator()
1971  def itervalues(self):
1972  return self.value_iterator()
1973  def iteritems(self):
1974  return self.iterator()
1975 
1976  def __getitem__(self, key):
1977  r"""__getitem__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key) -> AVPairDistanceMeasurement"""
1978  return _IMP_bff.MapStringAVPairDistanceMeasurement___getitem__(self, key)
1979 
1980  def __delitem__(self, key):
1981  r"""__delitem__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key)"""
1982  return _IMP_bff.MapStringAVPairDistanceMeasurement___delitem__(self, key)
1983 
1984  def has_key(self, key):
1985  r"""has_key(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key) -> bool"""
1986  return _IMP_bff.MapStringAVPairDistanceMeasurement_has_key(self, key)
1987 
1988  def keys(self):
1989  r"""keys(MapStringAVPairDistanceMeasurement self) -> PyObject *"""
1990  return _IMP_bff.MapStringAVPairDistanceMeasurement_keys(self)
1991 
1992  def values(self):
1993  r"""values(MapStringAVPairDistanceMeasurement self) -> PyObject *"""
1994  return _IMP_bff.MapStringAVPairDistanceMeasurement_values(self)
1995 
1996  def items(self):
1997  r"""items(MapStringAVPairDistanceMeasurement self) -> PyObject *"""
1998  return _IMP_bff.MapStringAVPairDistanceMeasurement_items(self)
1999 
2000  def __contains__(self, key):
2001  r"""__contains__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key) -> bool"""
2002  return _IMP_bff.MapStringAVPairDistanceMeasurement___contains__(self, key)
2003 
2004  def key_iterator(self):
2005  r"""key_iterator(MapStringAVPairDistanceMeasurement self) -> IMP_BFF_SwigPyIterator"""
2006  return _IMP_bff.MapStringAVPairDistanceMeasurement_key_iterator(self)
2007 
2008  def value_iterator(self):
2009  r"""value_iterator(MapStringAVPairDistanceMeasurement self) -> IMP_BFF_SwigPyIterator"""
2010  return _IMP_bff.MapStringAVPairDistanceMeasurement_value_iterator(self)
2011 
2012  def __setitem__(self, *args):
2013  r"""
2014  __setitem__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key)
2015  __setitem__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key, AVPairDistanceMeasurement x)
2016  """
2017  return _IMP_bff.MapStringAVPairDistanceMeasurement___setitem__(self, *args)
2018 
2019  def asdict(self):
2020  r"""asdict(MapStringAVPairDistanceMeasurement self) -> PyObject *"""
2021  return _IMP_bff.MapStringAVPairDistanceMeasurement_asdict(self)
2022 
2023  def __init__(self, *args):
2024  r"""
2025  __init__(MapStringAVPairDistanceMeasurement self, std::less< std::string > const & other) -> MapStringAVPairDistanceMeasurement
2026  __init__(MapStringAVPairDistanceMeasurement self) -> MapStringAVPairDistanceMeasurement
2027  __init__(MapStringAVPairDistanceMeasurement self, MapStringAVPairDistanceMeasurement other) -> MapStringAVPairDistanceMeasurement
2028  """
2029  _IMP_bff.MapStringAVPairDistanceMeasurement_swiginit(self, _IMP_bff.new_MapStringAVPairDistanceMeasurement(*args))
2030 
2031  def empty(self):
2032  r"""empty(MapStringAVPairDistanceMeasurement self) -> bool"""
2033  return _IMP_bff.MapStringAVPairDistanceMeasurement_empty(self)
2034 
2035  def size(self):
2036  r"""size(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::size_type"""
2037  return _IMP_bff.MapStringAVPairDistanceMeasurement_size(self)
2038 
2039  def swap(self, v):
2040  r"""swap(MapStringAVPairDistanceMeasurement self, MapStringAVPairDistanceMeasurement v)"""
2041  return _IMP_bff.MapStringAVPairDistanceMeasurement_swap(self, v)
2042 
2043  def begin(self):
2044  r"""begin(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2045  return _IMP_bff.MapStringAVPairDistanceMeasurement_begin(self)
2046 
2047  def end(self):
2048  r"""end(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2049  return _IMP_bff.MapStringAVPairDistanceMeasurement_end(self)
2050 
2051  def rbegin(self):
2052  r"""rbegin(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::reverse_iterator"""
2053  return _IMP_bff.MapStringAVPairDistanceMeasurement_rbegin(self)
2054 
2055  def rend(self):
2056  r"""rend(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::reverse_iterator"""
2057  return _IMP_bff.MapStringAVPairDistanceMeasurement_rend(self)
2058 
2059  def clear(self):
2060  r"""clear(MapStringAVPairDistanceMeasurement self)"""
2061  return _IMP_bff.MapStringAVPairDistanceMeasurement_clear(self)
2062 
2063  def get_allocator(self):
2064  r"""get_allocator(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::allocator_type"""
2065  return _IMP_bff.MapStringAVPairDistanceMeasurement_get_allocator(self)
2066 
2067  def count(self, x):
2068  r"""count(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::size_type"""
2069  return _IMP_bff.MapStringAVPairDistanceMeasurement_count(self, x)
2070 
2071  def erase(self, *args):
2072  r"""
2073  erase(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::size_type
2074  erase(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator position)
2075  erase(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator first, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator last)
2076  """
2077  return _IMP_bff.MapStringAVPairDistanceMeasurement_erase(self, *args)
2078 
2079  def find(self, x):
2080  r"""find(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2081  return _IMP_bff.MapStringAVPairDistanceMeasurement_find(self, x)
2082 
2083  def lower_bound(self, x):
2084  r"""lower_bound(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2085  return _IMP_bff.MapStringAVPairDistanceMeasurement_lower_bound(self, x)
2086 
2087  def upper_bound(self, x):
2088  r"""upper_bound(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2089  return _IMP_bff.MapStringAVPairDistanceMeasurement_upper_bound(self, x)
2090  __swig_destroy__ = _IMP_bff.delete_MapStringAVPairDistanceMeasurement
2091 
2092 # Register MapStringAVPairDistanceMeasurement in _IMP_bff:
2093 _IMP_bff.MapStringAVPairDistanceMeasurement_swigregister(MapStringAVPairDistanceMeasurement)
2094 DYE_PAIR_DISTANCE_E = _IMP_bff.DYE_PAIR_DISTANCE_E
2095 
2096 DYE_PAIR_DISTANCE_MEAN = _IMP_bff.DYE_PAIR_DISTANCE_MEAN
2097 
2098 DYE_PAIR_DISTANCE_MP = _IMP_bff.DYE_PAIR_DISTANCE_MP
2099 
2100 DYE_PAIR_EFFICIENCY = _IMP_bff.DYE_PAIR_EFFICIENCY
2101 
2102 DYE_PAIR_DISTANCE_DISTRIBUTION = _IMP_bff.DYE_PAIR_DISTANCE_DISTRIBUTION
2103 
2104 DYE_PAIR_XYZ_DISTANCE = _IMP_bff.DYE_PAIR_XYZ_DISTANCE
2105 
2106 class AVPairDistanceMeasurement(IMP._Value):
2107  r"""Proxy of C++ IMP::bff::AVPairDistanceMeasurement class."""
2108 
2109  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2110  distance = property(_IMP_bff.AVPairDistanceMeasurement_distance_get, _IMP_bff.AVPairDistanceMeasurement_distance_set, doc=r"""distance : double""")
2111  error_neg = property(_IMP_bff.AVPairDistanceMeasurement_error_neg_get, _IMP_bff.AVPairDistanceMeasurement_error_neg_set, doc=r"""error_neg : double""")
2112  error_pos = property(_IMP_bff.AVPairDistanceMeasurement_error_pos_get, _IMP_bff.AVPairDistanceMeasurement_error_pos_set, doc=r"""error_pos : double""")
2113  forster_radius = property(_IMP_bff.AVPairDistanceMeasurement_forster_radius_get, _IMP_bff.AVPairDistanceMeasurement_forster_radius_set, doc=r"""forster_radius : double""")
2114  distance_type = property(_IMP_bff.AVPairDistanceMeasurement_distance_type_get, _IMP_bff.AVPairDistanceMeasurement_distance_type_set, doc=r"""distance_type : int""")
2115  position_1 = property(_IMP_bff.AVPairDistanceMeasurement_position_1_get, _IMP_bff.AVPairDistanceMeasurement_position_1_set, doc=r"""position_1 : std::string""")
2116  position_2 = property(_IMP_bff.AVPairDistanceMeasurement_position_2_get, _IMP_bff.AVPairDistanceMeasurement_position_2_set, doc=r"""position_2 : std::string""")
2117 
2118  def get_json(self):
2119  r"""get_json(AVPairDistanceMeasurement self) -> std::string"""
2120  return _IMP_bff.AVPairDistanceMeasurement_get_json(self)
2121 
2122  def score_model(self, model):
2123  r"""score_model(AVPairDistanceMeasurement self, double model) -> double"""
2124  return _IMP_bff.AVPairDistanceMeasurement_score_model(self, model)
2125 
2126  def show(self, *args, **kwargs):
2127  r"""show(AVPairDistanceMeasurement self, _ostream out=std::cout)"""
2128  return _IMP_bff.AVPairDistanceMeasurement_show(self, *args, **kwargs)
2129 
2130  def __str__(self):
2131  r"""__str__(AVPairDistanceMeasurement self) -> std::string"""
2132  return _IMP_bff.AVPairDistanceMeasurement___str__(self)
2133 
2134  def __repr__(self):
2135  r"""__repr__(AVPairDistanceMeasurement self) -> std::string"""
2136  return _IMP_bff.AVPairDistanceMeasurement___repr__(self)
2137 
2138  def __init__(self):
2139  r"""__init__(AVPairDistanceMeasurement self) -> AVPairDistanceMeasurement"""
2140  _IMP_bff.AVPairDistanceMeasurement_swiginit(self, _IMP_bff.new_AVPairDistanceMeasurement())
2141  __swig_destroy__ = _IMP_bff.delete_AVPairDistanceMeasurement
2142 
2143 # Register AVPairDistanceMeasurement in _IMP_bff:
2144 _IMP_bff.AVPairDistanceMeasurement_swigregister(AVPairDistanceMeasurement)
2145 class AV(IMP.core.Gaussian):
2146  r"""Proxy of C++ IMP::bff::AV class."""
2147 
2148  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2149 
2150  def create_path_map_header(self):
2151  r"""create_path_map_header(AV self) -> PathMapHeader"""
2152  return _IMP_bff.AV_create_path_map_header(self)
2153 
2154  def init_path_map(self):
2155  r"""init_path_map(AV self)"""
2156  return _IMP_bff.AV_init_path_map(self)
2157 
2158  @staticmethod
2159  def get_av_key(i):
2160  r"""get_av_key(unsigned int i) -> FloatKey"""
2161  return _IMP_bff.AV_get_av_key(i)
2162 
2163  @staticmethod
2164  def do_setup_particle(*args, **kwargs):
2165  r"""do_setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_source, double linker_length=20.0, Vector3D radii=IMP::algebra::Vector3D(3.5, 0, 0), double linker_width=0.5, double allowed_sphere_radius=1.5, double contact_volume_thickness=0.0, double contact_volume_trapped_fraction=-1, double simulation_grid_resolution=1.5)"""
2166  return _IMP_bff.AV_do_setup_particle(*args, **kwargs)
2167 
2168  @staticmethod
2169  def get_particle_key(i):
2170  r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2171  return _IMP_bff.AV_get_particle_key(i)
2172 
2173  def get_particle_index(self, *args):
2174  r"""
2175  get_particle_index(AV self) -> ParticleIndex
2176  get_particle_index(AV self, unsigned int i) -> ParticleIndex
2177  """
2178  return _IMP_bff.AV_get_particle_index(self, *args)
2179 
2180  def get_particle(self, *args):
2181  r"""
2182  get_particle(AV self) -> Particle
2183  get_particle(AV self, unsigned int i) -> Particle
2184  """
2185  return _IMP_bff.AV_get_particle(self, *args)
2186 
2187  def __init__(self, *args):
2188  r"""
2189  __init__(AV self) -> AV
2190  __init__(AV self, Model m, ParticleIndex id) -> AV
2191  __init__(AV self, _ParticleAdaptor d) -> AV
2192  """
2193  _IMP_bff.AV_swiginit(self, _IMP_bff.new_AV(*args))
2194 
2195  def show(self, *args, **kwargs):
2196  r"""show(AV self, _ostream out=std::cout)"""
2197  return _IMP_bff.AV_show(self, *args, **kwargs)
2198 
2199  @staticmethod
2200  def setup_particle(*args):
2201  r"""
2202  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_source) -> AV
2203  setup_particle(_ParticleAdaptor pa, ParticleIndex pi_source) -> AV
2204  """
2205  return _IMP_bff.AV_setup_particle(*args)
2206 
2207  def get_linker_length(self):
2208  r"""get_linker_length(AV self) -> IMP::Float"""
2209  return _IMP_bff.AV_get_linker_length(self)
2210 
2211  def set_linker_length(self, t):
2212  r"""set_linker_length(AV self, IMP::Float t)"""
2213  return _IMP_bff.AV_set_linker_length(self, t)
2214 
2215  def get_radius1(self):
2216  r"""get_radius1(AV self) -> IMP::Float"""
2217  return _IMP_bff.AV_get_radius1(self)
2218 
2219  def set_radius1(self, t):
2220  r"""set_radius1(AV self, IMP::Float t)"""
2221  return _IMP_bff.AV_set_radius1(self, t)
2222 
2223  def get_radius2(self):
2224  r"""get_radius2(AV self) -> IMP::Float"""
2225  return _IMP_bff.AV_get_radius2(self)
2226 
2227  def set_radius2(self, t):
2228  r"""set_radius2(AV self, IMP::Float t)"""
2229  return _IMP_bff.AV_set_radius2(self, t)
2230 
2231  def get_radius3(self):
2232  r"""get_radius3(AV self) -> IMP::Float"""
2233  return _IMP_bff.AV_get_radius3(self)
2234 
2235  def set_radius3(self, t):
2236  r"""set_radius3(AV self, IMP::Float t)"""
2237  return _IMP_bff.AV_set_radius3(self, t)
2238 
2239  def get_linker_width(self):
2240  r"""get_linker_width(AV self) -> IMP::Float"""
2241  return _IMP_bff.AV_get_linker_width(self)
2242 
2243  def set_linker_width(self, t):
2244  r"""set_linker_width(AV self, IMP::Float t)"""
2245  return _IMP_bff.AV_set_linker_width(self, t)
2246 
2247  def get_allowed_sphere_radius(self):
2248  r"""get_allowed_sphere_radius(AV self) -> IMP::Float"""
2249  return _IMP_bff.AV_get_allowed_sphere_radius(self)
2250 
2251  def set_allowed_sphere_radius(self, t):
2252  r"""set_allowed_sphere_radius(AV self, IMP::Float t)"""
2253  return _IMP_bff.AV_set_allowed_sphere_radius(self, t)
2254 
2255  def get_contact_volume_thickness(self):
2256  r"""get_contact_volume_thickness(AV self) -> IMP::Float"""
2257  return _IMP_bff.AV_get_contact_volume_thickness(self)
2258 
2259  def set_contact_volume_thickness(self, t):
2260  r"""set_contact_volume_thickness(AV self, IMP::Float t)"""
2261  return _IMP_bff.AV_set_contact_volume_thickness(self, t)
2262 
2263  def get_contact_volume_trapped_fraction(self):
2264  r"""get_contact_volume_trapped_fraction(AV self) -> IMP::Float"""
2265  return _IMP_bff.AV_get_contact_volume_trapped_fraction(self)
2266 
2267  def set_contact_volume_trapped_fraction(self, t):
2268  r"""set_contact_volume_trapped_fraction(AV self, IMP::Float t)"""
2269  return _IMP_bff.AV_set_contact_volume_trapped_fraction(self, t)
2270 
2271  def get_simulation_grid_resolution(self):
2272  r"""get_simulation_grid_resolution(AV self) -> IMP::Float"""
2273  return _IMP_bff.AV_get_simulation_grid_resolution(self)
2274 
2275  def set_simulation_grid_resolution(self, t):
2276  r"""set_simulation_grid_resolution(AV self, IMP::Float t)"""
2277  return _IMP_bff.AV_set_simulation_grid_resolution(self, t)
2278 
2279  def get_radii(self):
2280  r"""get_radii(AV self) -> Vector3D"""
2281  return _IMP_bff.AV_get_radii(self)
2282 
2283  def get_parameters_are_optimized(self):
2284  r"""get_parameters_are_optimized(AV self) -> bool"""
2285  return _IMP_bff.AV_get_parameters_are_optimized(self)
2286 
2287  def set_av_parameters_are_optimized(self, tf):
2288  r"""set_av_parameters_are_optimized(AV self, bool tf)"""
2289  return _IMP_bff.AV_set_av_parameters_are_optimized(self, tf)
2290 
2291  def set_av_parameter(self, j):
2292  r"""set_av_parameter(AV self, nlohmann::json const & j)"""
2293  return _IMP_bff.AV_set_av_parameter(self, j)
2294 
2295  def get_derivatives(self):
2296  r"""get_derivatives(AV self) -> Vector3D"""
2297  return _IMP_bff.AV_get_derivatives(self)
2298 
2299  @staticmethod
2300  def get_is_setup(*args):
2301  r"""
2302  get_is_setup(_ParticleAdaptor p) -> bool
2303  get_is_setup(Model m, ParticleIndex pi) -> bool
2304  """
2305  return _IMP_bff.AV_get_is_setup(*args)
2306 
2307  def get_map(self):
2308  r"""get_map(AV self) -> PathMap"""
2309  return _IMP_bff.AV_get_map(self)
2310 
2311  def resample(self, shift_xyz=True):
2312  r"""resample(AV self, bool shift_xyz=True)"""
2313  return _IMP_bff.AV_resample(self, shift_xyz)
2314 
2315  def get_mean_position(self, include_source=True):
2316  r"""get_mean_position(AV self, bool include_source=True) -> Vector3D"""
2317  return _IMP_bff.AV_get_mean_position(self, include_source)
2318 
2319  def get_source_coordinates(self):
2320  r"""get_source_coordinates(AV self) -> Vector3D"""
2321  return _IMP_bff.AV_get_source_coordinates(self)
2322 
2323  def get_source(self):
2324  r"""get_source(AV self) -> Particle"""
2325  return _IMP_bff.AV_get_source(self)
2326 
2327  def add_attribute(self, *args):
2328  r"""
2329  add_attribute(AV self, FloatKey k, IMP::Float v, bool opt)
2330  add_attribute(AV self, FloatKey a0, IMP::Float a1)
2331  add_attribute(AV self, IntKey a0, IMP::Int a1)
2332  add_attribute(AV self, FloatsKey a0, IMP::Floats a1)
2333  add_attribute(AV self, IntsKey a0, IMP::Ints a1)
2334  add_attribute(AV self, StringKey a0, IMP::String a1)
2335  add_attribute(AV self, ParticleIndexKey a0, Particle a1)
2336  add_attribute(AV self, ObjectKey a0, Object a1)
2337  add_attribute(AV self, SparseFloatKey a0, IMP::Float a1)
2338  add_attribute(AV self, SparseIntKey a0, IMP::Int a1)
2339  add_attribute(AV self, SparseStringKey a0, IMP::String a1)
2340  add_attribute(AV self, SparseParticleIndexKey a0, ParticleIndex a1)
2341  """
2342  return _IMP_bff.AV_add_attribute(self, *args)
2343 
2344  def get_value(self, *args):
2345  r"""
2346  get_value(AV self, FloatKey a0) -> IMP::Float
2347  get_value(AV self, IntKey a0) -> IMP::Int
2348  get_value(AV self, FloatsKey a0) -> IMP::Floats
2349  get_value(AV self, IntsKey a0) -> IMP::Ints
2350  get_value(AV self, StringKey a0) -> IMP::String
2351  get_value(AV self, ParticleIndexKey a0) -> Particle
2352  get_value(AV self, ObjectKey a0) -> Object
2353  get_value(AV self, SparseFloatKey a0) -> IMP::Float
2354  get_value(AV self, SparseIntKey a0) -> IMP::Int
2355  get_value(AV self, SparseStringKey a0) -> IMP::String
2356  get_value(AV self, SparseParticleIndexKey a0) -> ParticleIndex
2357  """
2358  return _IMP_bff.AV_get_value(self, *args)
2359 
2360  def set_value(self, *args):
2361  r"""
2362  set_value(AV self, FloatKey a0, IMP::Float a1)
2363  set_value(AV self, IntKey a0, IMP::Int a1)
2364  set_value(AV self, FloatsKey a0, IMP::Floats a1)
2365  set_value(AV self, IntsKey a0, IMP::Ints a1)
2366  set_value(AV self, StringKey a0, IMP::String a1)
2367  set_value(AV self, ParticleIndexKey a0, Particle a1)
2368  set_value(AV self, ObjectKey a0, Object a1)
2369  set_value(AV self, SparseFloatKey a0, IMP::Float a1)
2370  set_value(AV self, SparseIntKey a0, IMP::Int a1)
2371  set_value(AV self, SparseStringKey a0, IMP::String a1)
2372  set_value(AV self, SparseParticleIndexKey a0, ParticleIndex a1)
2373  """
2374  return _IMP_bff.AV_set_value(self, *args)
2375 
2376  def remove_attribute(self, *args):
2377  r"""
2378  remove_attribute(AV self, FloatKey a0)
2379  remove_attribute(AV self, IntKey a0)
2380  remove_attribute(AV self, FloatsKey a0)
2381  remove_attribute(AV self, IntsKey a0)
2382  remove_attribute(AV self, StringKey a0)
2383  remove_attribute(AV self, ParticleIndexKey a0)
2384  remove_attribute(AV self, ObjectKey a0)
2385  remove_attribute(AV self, SparseFloatKey a0)
2386  remove_attribute(AV self, SparseIntKey a0)
2387  remove_attribute(AV self, SparseStringKey a0)
2388  remove_attribute(AV self, SparseParticleIndexKey a0)
2389  """
2390  return _IMP_bff.AV_remove_attribute(self, *args)
2391 
2392  def has_attribute(self, *args):
2393  r"""
2394  has_attribute(AV self, FloatKey a0) -> bool
2395  has_attribute(AV self, IntKey a0) -> bool
2396  has_attribute(AV self, FloatsKey a0) -> bool
2397  has_attribute(AV self, IntsKey a0) -> bool
2398  has_attribute(AV self, StringKey a0) -> bool
2399  has_attribute(AV self, ParticleIndexKey a0) -> bool
2400  has_attribute(AV self, ObjectKey a0) -> bool
2401  has_attribute(AV self, SparseFloatKey a0) -> bool
2402  has_attribute(AV self, SparseIntKey a0) -> bool
2403  has_attribute(AV self, SparseStringKey a0) -> bool
2404  has_attribute(AV self, SparseParticleIndexKey a0) -> bool
2405  """
2406  return _IMP_bff.AV_has_attribute(self, *args)
2407 
2408  def get_derivative(self, a0):
2409  r"""get_derivative(AV self, FloatKey a0) -> double"""
2410  return _IMP_bff.AV_get_derivative(self, a0)
2411 
2412  def get_name(self):
2413  r"""get_name(AV self) -> std::string"""
2414  return _IMP_bff.AV_get_name(self)
2415 
2416  def clear_caches(self):
2417  r"""clear_caches(AV self)"""
2418  return _IMP_bff.AV_clear_caches(self)
2419 
2420  def set_name(self, a0):
2421  r"""set_name(AV self, std::string a0)"""
2422  return _IMP_bff.AV_set_name(self, a0)
2423 
2424  def set_check_level(self, a0):
2425  r"""set_check_level(AV self, IMP::CheckLevel a0)"""
2426  return _IMP_bff.AV_set_check_level(self, a0)
2427 
2428  def add_to_derivative(self, a0, a1, a2):
2429  r"""add_to_derivative(AV self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2430  return _IMP_bff.AV_add_to_derivative(self, a0, a1, a2)
2431 
2432  def set_is_optimized(self, a0, a1):
2433  r"""set_is_optimized(AV self, FloatKey a0, bool a1)"""
2434  return _IMP_bff.AV_set_is_optimized(self, a0, a1)
2435 
2436  def get_is_optimized(self, a0):
2437  r"""get_is_optimized(AV self, FloatKey a0) -> bool"""
2438  return _IMP_bff.AV_get_is_optimized(self, a0)
2439 
2440  def get_check_level(self):
2441  r"""get_check_level(AV self) -> IMP::CheckLevel"""
2442  return _IMP_bff.AV_get_check_level(self)
2443 
2444  def __eq__(self, *args):
2445  r"""
2446  __eq__(AV self, AV o) -> bool
2447  __eq__(AV self, Particle d) -> bool
2448  """
2449  return _IMP_bff.AV___eq__(self, *args)
2450 
2451  def __ne__(self, *args):
2452  r"""
2453  __ne__(AV self, AV o) -> bool
2454  __ne__(AV self, Particle d) -> bool
2455  """
2456  return _IMP_bff.AV___ne__(self, *args)
2457 
2458  def __le__(self, *args):
2459  r"""
2460  __le__(AV self, AV o) -> bool
2461  __le__(AV self, Particle d) -> bool
2462  """
2463  return _IMP_bff.AV___le__(self, *args)
2464 
2465  def __lt__(self, *args):
2466  r"""
2467  __lt__(AV self, AV o) -> bool
2468  __lt__(AV self, Particle d) -> bool
2469  """
2470  return _IMP_bff.AV___lt__(self, *args)
2471 
2472  def __ge__(self, *args):
2473  r"""
2474  __ge__(AV self, AV o) -> bool
2475  __ge__(AV self, Particle d) -> bool
2476  """
2477  return _IMP_bff.AV___ge__(self, *args)
2478 
2479  def __gt__(self, *args):
2480  r"""
2481  __gt__(AV self, AV o) -> bool
2482  __gt__(AV self, Particle d) -> bool
2483  """
2484  return _IMP_bff.AV___gt__(self, *args)
2485 
2486  def __hash__(self):
2487  r"""__hash__(AV self) -> std::size_t"""
2488  return _IMP_bff.AV___hash__(self)
2489 
2490  def __str__(self):
2491  r"""__str__(AV self) -> std::string"""
2492  return _IMP_bff.AV___str__(self)
2493 
2494  def __repr__(self):
2495  r"""__repr__(AV self) -> std::string"""
2496  return _IMP_bff.AV___repr__(self)
2497 
2498  def _get_as_binary(self):
2499  r"""_get_as_binary(AV self) -> PyObject *"""
2500  return _IMP_bff.AV__get_as_binary(self)
2501 
2502  def _set_from_binary(self, p):
2503  r"""_set_from_binary(AV self, PyObject * p)"""
2504  return _IMP_bff.AV__set_from_binary(self, p)
2505 
2506  def __getstate__(self):
2507  p = self._get_as_binary()
2508  if len(self.__dict__) > 1:
2509  d = self.__dict__.copy()
2510  del d['this']
2511  p = (d, p)
2512  return p
2513 
2514  def __setstate__(self, p):
2515  if not hasattr(self, 'this'):
2516  self.__init__()
2517  if isinstance(p, tuple):
2518  d, p = p
2519  self.__dict__.update(d)
2520  return self._set_from_binary(p)
2521 
2522 
2523  map = property(get_map)
2524 
2525  __swig_destroy__ = _IMP_bff.delete_AV
2526 
2527 # Register AV in _IMP_bff:
2528 _IMP_bff.AV_swigregister(AV)
2529 
2530 def __lshift__(out, n):
2531  r"""__lshift__(_ostream out, AV n) -> _ostream"""
2532  return _IMP_bff.__lshift__(out, n)
2533 
2534 def av_distance(*args, **kwargs):
2535  r"""av_distance(AV a, AV b, double forster_radius=52.0, int distance_type=DYE_PAIR_DISTANCE_MEAN, int n_samples=10000) -> double"""
2536  return _IMP_bff.av_distance(*args, **kwargs)
2537 
2538 def av_random_points(av1, n_samples=10000):
2539  r"""av_random_points(AV av1, int n_samples=10000) -> VectorDouble"""
2540  return _IMP_bff.av_random_points(av1, n_samples)
2541 
2542 def av_random_distances(av1, av2, n_samples=10000):
2543  r"""av_random_distances(AV av1, AV av2, int n_samples=10000) -> VectorDouble"""
2544  return _IMP_bff.av_random_distances(av1, av2, n_samples)
2545 
2546 def av_distance_distribution(av1, av2, axis, n_samples=10000):
2547  r"""av_distance_distribution(AV av1, AV av2, VectorDouble axis, int n_samples=10000) -> VectorDouble"""
2548  return _IMP_bff.av_distance_distribution(av1, av2, axis, n_samples)
2549 
2550 def search_labeling_site(*args, **kwargs):
2551  r"""search_labeling_site(Hierarchy hier, std::string json_str="", nlohmann::json const & json_data=nlohmann::json()) -> ParticleIndex"""
2552  return _IMP_bff.search_labeling_site(*args, **kwargs)
2553 class AVNetworkRestraint(IMP.Restraint):
2554  r"""Proxy of C++ IMP::bff::AVNetworkRestraint class."""
2555 
2556  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2557 
2558  def __init__(self, *args, **kwargs):
2559  r"""__init__(AVNetworkRestraint self, Hierarchy hier, std::string fps_json_fn, std::string name="AVNetworkRestraint%1%", std::string score_set="", int n_samples=50000) -> AVNetworkRestraint"""
2560  _IMP_bff.AVNetworkRestraint_swiginit(self, _IMP_bff.new_AVNetworkRestraint(*args, **kwargs))
2561 
2562  def get_probability(self):
2563  r"""get_probability(AVNetworkRestraint self) -> double"""
2564  return _IMP_bff.AVNetworkRestraint_get_probability(self)
2565 
2566  def get_used_avs(self):
2567  r"""get_used_avs(AVNetworkRestraint self) -> IMP::bff::AVs const"""
2568  return _IMP_bff.AVNetworkRestraint_get_used_avs(self)
2569 
2570  def get_used_distances(self):
2571  r"""get_used_distances(AVNetworkRestraint self) -> MapStringAVPairDistanceMeasurement"""
2572  return _IMP_bff.AVNetworkRestraint_get_used_distances(self)
2573 
2574  def get_model_distance(self, position1_name, position2_name, forster_radius, distance_type):
2575  r"""get_model_distance(AVNetworkRestraint self, std::string position1_name, std::string position2_name, double forster_radius, int distance_type) -> double"""
2576  return _IMP_bff.AVNetworkRestraint_get_model_distance(self, position1_name, position2_name, forster_radius, distance_type)
2577 
2578  def get_indexes(self):
2579  r"""get_indexes(AVNetworkRestraint self) -> IMP::ParticleIndexes const"""
2580  return _IMP_bff.AVNetworkRestraint_get_indexes(self)
2581 
2582  def do_get_inputs(self):
2583  r"""do_get_inputs(AVNetworkRestraint self) -> IMP::ModelObjectsTemp"""
2584  return _IMP_bff.AVNetworkRestraint_do_get_inputs(self)
2585 
2586  def show(self, out):
2587  r"""show(AVNetworkRestraint self, _ostream out)"""
2588  return _IMP_bff.AVNetworkRestraint_show(self, out)
2589 
2590  def get_version_info(self):
2591  r"""get_version_info(AVNetworkRestraint self) -> VersionInfo"""
2592  return _IMP_bff.AVNetworkRestraint_get_version_info(self)
2593  __swig_destroy__ = _IMP_bff.delete_AVNetworkRestraint
2594 
2595  def __str__(self):
2596  r"""__str__(AVNetworkRestraint self) -> std::string"""
2597  return _IMP_bff.AVNetworkRestraint___str__(self)
2598 
2599  def __repr__(self):
2600  r"""__repr__(AVNetworkRestraint self) -> std::string"""
2601  return _IMP_bff.AVNetworkRestraint___repr__(self)
2602 
2603  @staticmethod
2604  def get_from(o):
2605  return _object_cast_to_AVNetworkRestraint(o)
2606 
2607 
2608 # Register AVNetworkRestraint in _IMP_bff:
2609 _IMP_bff.AVNetworkRestraint_swigregister(AVNetworkRestraint)
2610 
2611 def decay_rescale(fit, decay, start=0, stop=-1):
2612  r"""decay_rescale(double * fit, double * decay, int start=0, int stop=-1) -> double"""
2613  return _IMP_bff.decay_rescale(fit, decay, start, stop)
2614 
2615 def decay_rescale_w(fit, decay, w_sq, start=0, stop=-1):
2616  r"""decay_rescale_w(double * fit, double * decay, double * w_sq, int start=0, int stop=-1) -> double"""
2617  return _IMP_bff.decay_rescale_w(fit, decay, w_sq, start, stop)
2618 
2619 def decay_rescale_w_bg(fit, decay, w_sq, bg=0.0, start=0, stop=-1):
2620  r"""decay_rescale_w_bg(double * fit, double * decay, double * w_sq, double bg=0.0, int start=0, int stop=-1) -> double"""
2621  return _IMP_bff.decay_rescale_w_bg(fit, decay, w_sq, bg, start, stop)
2622 
2623 def decay_fconv(fit, irf, x, start=0, stop=-1, dt=1.0):
2624  r"""decay_fconv(double * fit, double * irf, double * x, int start=0, int stop=-1, double dt=1.0)"""
2625  return _IMP_bff.decay_fconv(fit, irf, x, start, stop, dt)
2626 
2627 def decay_fconv_avx(fit, irf, x, start=0, stop=-1, dt=1.0):
2628  r"""decay_fconv_avx(double * fit, double * irf, double * x, int start=0, int stop=-1, double dt=1.0)"""
2629  return _IMP_bff.decay_fconv_avx(fit, irf, x, start, stop, dt)
2630 
2631 def decay_fconv_per(fit, irf, x, period, start=0, stop=-1, dt=1.0):
2632  r"""decay_fconv_per(double * fit, double * irf, double * x, double period, int start=0, int stop=-1, double dt=1.0)"""
2633  return _IMP_bff.decay_fconv_per(fit, irf, x, period, start, stop, dt)
2634 
2635 def decay_fconv_per_avx(fit, irf, x, period, start=0, stop=-1, dt=1.0):
2636  r"""decay_fconv_per_avx(double * fit, double * irf, double * x, double period, int start=0, int stop=-1, double dt=1.0)"""
2637  return _IMP_bff.decay_fconv_per_avx(fit, irf, x, period, start, stop, dt)
2638 
2639 def decay_fconv_per_cs(fit, irf, x, period, conv_stop=-1, stop=-1, dt=1.0):
2640  r"""decay_fconv_per_cs(double * fit, double * irf, double * x, double period, int conv_stop=-1, int stop=-1, double dt=1.0)"""
2641  return _IMP_bff.decay_fconv_per_cs(fit, irf, x, period, conv_stop, stop, dt)
2642 
2643 def decay_fconv_ref(fit, irf, x, tauref, start=0, stop=-1, dt=1.0):
2644  r"""decay_fconv_ref(double * fit, double * irf, double * x, double tauref, int start=0, int stop=-1, double dt=1.0)"""
2645  return _IMP_bff.decay_fconv_ref(fit, irf, x, tauref, start, stop, dt)
2646 
2647 def decay_sconv(fit, irf, model, start=0, stop=-1):
2648  r"""decay_sconv(double * fit, double * irf, double * model, int start=0, int stop=-1)"""
2649  return _IMP_bff.decay_sconv(fit, irf, model, start, stop)
2650 
2651 def decay_shift_lamp(irf, irf_shift, ts):
2652  r"""decay_shift_lamp(double * irf, double * irf_shift, double ts)"""
2653  return _IMP_bff.decay_shift_lamp(irf, irf_shift, ts)
2654 
2655 def mod_p(a, n):
2656  r"""mod_p(int a, int n) -> int"""
2657  return _IMP_bff.mod_p(a, n)
2658 
2659 def decay_add_pile_up_to_model(*args, **kwargs):
2660  r"""decay_add_pile_up_to_model(double * model, double * data, double repetition_rate, double instrument_dead_time, double measurement_time, std::string pile_up_model="coates", int start=0, int stop=-1)"""
2661  return _IMP_bff.decay_add_pile_up_to_model(*args, **kwargs)
2662 
2663 def discriminate_small_amplitudes(lifetime_spectrum, amplitude_threshold):
2664  r"""discriminate_small_amplitudes(double * lifetime_spectrum, double amplitude_threshold)"""
2665  return _IMP_bff.discriminate_small_amplitudes(lifetime_spectrum, amplitude_threshold)
2666 
2667 def decay_fconv_per_cs_time_axis(model, time_axis, irf, lifetime_spectrum, convolution_start=0, convolution_stop=-1, period=100.0):
2668  r"""decay_fconv_per_cs_time_axis(double * model, double * time_axis, double * irf, double * lifetime_spectrum, int convolution_start=0, int convolution_stop=-1, double period=100.0)"""
2669  return _IMP_bff.decay_fconv_per_cs_time_axis(model, time_axis, irf, lifetime_spectrum, convolution_start, convolution_stop, period)
2670 
2671 def decay_fconv_cs_time_axis(inplace_output, time_axis, irf, lifetime_spectrum, convolution_start=0, convolution_stop=-1):
2672  r"""decay_fconv_cs_time_axis(double * inplace_output, double * time_axis, double * irf, double * lifetime_spectrum, int convolution_start=0, int convolution_stop=-1)"""
2673  return _IMP_bff.decay_fconv_cs_time_axis(inplace_output, time_axis, irf, lifetime_spectrum, convolution_start, convolution_stop)
2674 NOISE_NA = _IMP_bff.NOISE_NA
2675 
2676 NOISE_POISSON = _IMP_bff.NOISE_POISSON
2677 
2678 class DecayCurve(object):
2679  r"""Proxy of C++ IMP::bff::DecayCurve class."""
2680 
2681  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2682  __repr__ = _swig_repr
2683 
2684  @staticmethod
2685  def shift_array(input, shift):
2686  r"""shift_array(double * input, double shift) -> VectorDouble"""
2687  return _IMP_bff.DecayCurve_shift_array(input, shift)
2688 
2689  def size(self):
2690  r"""size(DecayCurve self) -> size_t"""
2691  return _IMP_bff.DecayCurve_size(self)
2692 
2693  def empty(self):
2694  r"""empty(DecayCurve self) -> bool"""
2695  return _IMP_bff.DecayCurve_empty(self)
2696 
2697  def get_dx(self):
2698  r"""get_dx(DecayCurve self) -> VectorDouble"""
2699  return _IMP_bff.DecayCurve_get_dx(self)
2700 
2701  def resize(self, n, v=0.0, dx=1.0):
2702  r"""resize(DecayCurve self, size_t n, double v=0.0, double dx=1.0)"""
2703  return _IMP_bff.DecayCurve_resize(self, n, v, dx)
2704 
2705  def get_average_dx(self):
2706  r"""get_average_dx(DecayCurve self) -> double"""
2707  return _IMP_bff.DecayCurve_get_average_dx(self)
2708 
2709  def get_x(self):
2710  r"""get_x(DecayCurve self) -> VectorDouble"""
2711  return _IMP_bff.DecayCurve_get_x(self)
2712 
2713  def set_x(self, *args):
2714  r"""
2715  set_x(DecayCurve self, VectorDouble v)
2716  set_x(DecayCurve self, double * input)
2717  """
2718  return _IMP_bff.DecayCurve_set_x(self, *args)
2719 
2720  def get_y(self):
2721  r"""get_y(DecayCurve self) -> VectorDouble"""
2722  return _IMP_bff.DecayCurve_get_y(self)
2723 
2724  def set_y(self, *args):
2725  r"""
2726  set_y(DecayCurve self, VectorDouble v)
2727  set_y(DecayCurve self, double * input)
2728  """
2729  return _IMP_bff.DecayCurve_set_y(self, *args)
2730 
2731  def get_ey(self):
2732  r"""get_ey(DecayCurve self) -> VectorDouble"""
2733  return _IMP_bff.DecayCurve_get_ey(self)
2734 
2735  def set_ey(self, *args):
2736  r"""
2737  set_ey(DecayCurve self, VectorDouble v)
2738  set_ey(DecayCurve self, double * input)
2739  """
2740  return _IMP_bff.DecayCurve_set_ey(self, *args)
2741 
2742  def set_acquisition_time(self, v):
2743  r"""set_acquisition_time(DecayCurve self, double v)"""
2744  return _IMP_bff.DecayCurve_set_acquisition_time(self, v)
2745 
2746  def get_acquisition_time(self):
2747  r"""get_acquisition_time(DecayCurve self) -> double"""
2748  return _IMP_bff.DecayCurve_get_acquisition_time(self)
2749 
2750  def set_shift(self, v):
2751  r"""set_shift(DecayCurve self, double v)"""
2752  return _IMP_bff.DecayCurve_set_shift(self, v)
2753 
2754  def get_shift(self):
2755  r"""get_shift(DecayCurve self) -> double"""
2756  return _IMP_bff.DecayCurve_get_shift(self)
2757 
2758  def get_json(self):
2759  r"""get_json(DecayCurve self) -> std::string"""
2760  return _IMP_bff.DecayCurve_get_json(self)
2761 
2762  def read_json(self, json_string):
2763  r"""read_json(DecayCurve self, std::string json_string) -> int"""
2764  return _IMP_bff.DecayCurve_read_json(self, json_string)
2765 
2766  def __init__(self, *args, **kwargs):
2767  r"""__init__(DecayCurve self, VectorDouble x=std::vector< double >(), VectorDouble y=std::vector< double >(), VectorDouble ey=std::vector< double >(), double acquisition_time=std::numeric_limits< double >::max(), int noise_model=NOISE_POISSON, int size=-1) -> DecayCurve"""
2768  _IMP_bff.DecayCurve_swiginit(self, _IMP_bff.new_DecayCurve(*args, **kwargs))
2769 
2770  def sum(self, start=0, stop=-1):
2771  r"""sum(DecayCurve self, int start=0, int stop=-1) -> double"""
2772  return _IMP_bff.DecayCurve_sum(self, start, stop)
2773 
2774  def apply_simple_moving_average(self, start, stop, n_window=5, normalize=False):
2775  r"""apply_simple_moving_average(DecayCurve self, int start, int stop, int n_window=5, bool normalize=False)"""
2776  return _IMP_bff.DecayCurve_apply_simple_moving_average(self, start, stop, n_window, normalize)
2777 
2778  def __iadd__(self, v):
2779  r"""__iadd__(DecayCurve self, double v) -> DecayCurve"""
2780  return _IMP_bff.DecayCurve___iadd__(self, v)
2781 
2782  def __isub__(self, v):
2783  r"""__isub__(DecayCurve self, double v) -> DecayCurve"""
2784  return _IMP_bff.DecayCurve___isub__(self, v)
2785 
2786  def __imul__(self, v):
2787  r"""__imul__(DecayCurve self, double v) -> DecayCurve"""
2788  return _IMP_bff.DecayCurve___imul__(self, v)
2789 
2790  def __itruediv__(self, *args):
2791  return _IMP_bff.DecayCurve___itruediv__(self, *args)
2792  __idiv__ = __itruediv__
2793 
2794 
2795 
2796  def __add__(self, *args):
2797  r"""
2798  __add__(DecayCurve self, double v) -> DecayCurve
2799  __add__(DecayCurve self, DecayCurve other) -> DecayCurve
2800  """
2801  return _IMP_bff.DecayCurve___add__(self, *args)
2802 
2803  def __sub__(self, *args):
2804  r"""
2805  __sub__(DecayCurve self, double v) -> DecayCurve
2806  __sub__(DecayCurve self, DecayCurve other) -> DecayCurve
2807  """
2808  return _IMP_bff.DecayCurve___sub__(self, *args)
2809 
2810  def __mul__(self, *args):
2811  r"""
2812  __mul__(DecayCurve self, double v) -> DecayCurve
2813  __mul__(DecayCurve self, DecayCurve other) -> DecayCurve
2814  """
2815  return _IMP_bff.DecayCurve___mul__(self, *args)
2816 
2817  def __truediv__(self, *args):
2818  return _IMP_bff.DecayCurve___truediv__(self, *args)
2819  __div__ = __truediv__
2820 
2821 
2822 
2823  def __lshift__(self, v):
2824  r"""__lshift__(DecayCurve self, double v) -> DecayCurve"""
2825  return _IMP_bff.DecayCurve___lshift__(self, v)
2826 
2827  acquisition_time = property(get_acquisition_time, set_acquisition_time)
2828 
2829 
2830  shift = property(get_shift, set_shift)
2831 
2832 
2833  x = property(
2834  lambda x: np.array(x.get_x()),
2835  set_x
2836  )
2837 
2838 
2839  y = property(
2840  lambda x: np.array(x.get_y()),
2841  set_y
2842  )
2843 
2844 
2845  ey = property(
2846  lambda x: np.array(x.get_ey()),
2847  set_ey
2848  )
2849 
2850  __swig_destroy__ = _IMP_bff.delete_DecayCurve
2851 
2852 # Register DecayCurve in _IMP_bff:
2853 _IMP_bff.DecayCurve_swigregister(DecayCurve)
2854 
2855 DecayRanges=list
2856 _plural_types.append("DecayRanges")
2857 _value_types.append("DecayRange")
2858 
2859 class DecayRange(IMP._Value):
2860  r"""Proxy of C++ IMP::bff::DecayRange class."""
2861 
2862  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2863 
2864  def get_start(self, d=None):
2865  r"""get_start(DecayRange self, DecayCurve d=None) -> size_t"""
2866  return _IMP_bff.DecayRange_get_start(self, d)
2867 
2868  def get_stop(self, d=None):
2869  r"""get_stop(DecayRange self, DecayCurve d=None) -> size_t"""
2870  return _IMP_bff.DecayRange_get_stop(self, d)
2871 
2872  def set_range(self, v):
2873  r"""set_range(DecayRange self, VectorInt v)"""
2874  return _IMP_bff.DecayRange_set_range(self, v)
2875 
2876  def get_range(self, d=None):
2877  r"""get_range(DecayRange self, DecayCurve d=None) -> VectorInt"""
2878  return _IMP_bff.DecayRange_get_range(self, d)
2879 
2880  def set(self, start=0, stop=-1):
2881  r"""set(DecayRange self, int start=0, int stop=-1)"""
2882  return _IMP_bff.DecayRange_set(self, start, stop)
2883 
2884  def __init__(self, start, stop):
2885  r"""__init__(DecayRange self, int start, int stop) -> DecayRange"""
2886  _IMP_bff.DecayRange_swiginit(self, _IMP_bff.new_DecayRange(start, stop))
2887  __swig_destroy__ = _IMP_bff.delete_DecayRange
2888 
2889  def show(self, *args, **kwargs):
2890  r"""show(DecayRange self, _ostream out=std::cout)"""
2891  return _IMP_bff.DecayRange_show(self, *args, **kwargs)
2892 
2893  def __str__(self):
2894  r"""__str__(DecayRange self) -> std::string"""
2895  return _IMP_bff.DecayRange___str__(self)
2896 
2897  def __repr__(self):
2898  r"""__repr__(DecayRange self) -> std::string"""
2899  return _IMP_bff.DecayRange___repr__(self)
2900  start = property(_IMP_bff.DecayRange_start_get, _IMP_bff.DecayRange_start_set, doc=r"""start : int""")
2901  stop = property(_IMP_bff.DecayRange_stop_get, _IMP_bff.DecayRange_stop_set, doc=r"""stop : int""")
2902 
2903 # Register DecayRange in _IMP_bff:
2904 _IMP_bff.DecayRange_swigregister(DecayRange)
2905 
2906 _object_types.append("DecayLifetimeHandler")
2907 
2908 
2909 def _object_cast_to_DecayLifetimeHandler(o):
2910  r"""_object_cast_to_DecayLifetimeHandler(Object o) -> DecayLifetimeHandler"""
2911  return _IMP_bff._object_cast_to_DecayLifetimeHandler(o)
2912 class DecayLifetimeHandler(IMP.Object):
2913  r"""Proxy of C++ IMP::bff::DecayLifetimeHandler class."""
2914 
2915  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2916 
2917  def add_lifetime(self, amplitude, lifetime):
2918  r"""add_lifetime(DecayLifetimeHandler self, double amplitude, double lifetime)"""
2919  return _IMP_bff.DecayLifetimeHandler_add_lifetime(self, amplitude, lifetime)
2920 
2921  def get_lifetime_spectrum(self):
2922  r"""get_lifetime_spectrum(DecayLifetimeHandler self)"""
2923  return _IMP_bff.DecayLifetimeHandler_get_lifetime_spectrum(self)
2924 
2925  def __init__(self, *args, **kwargs):
2926  r"""__init__(DecayLifetimeHandler self, VectorDouble lifetime_spectrum=std::vector< double >(), bool use_amplitude_threshold=False, bool abs_lifetime_spectrum=False, double amplitude_threshold=std::numeric_limits< double >::epsilon()) -> DecayLifetimeHandler"""
2927  _IMP_bff.DecayLifetimeHandler_swiginit(self, _IMP_bff.new_DecayLifetimeHandler(*args, **kwargs))
2928 
2929  def get_version_info(self):
2930  r"""get_version_info(DecayLifetimeHandler self) -> VersionInfo"""
2931  return _IMP_bff.DecayLifetimeHandler_get_version_info(self)
2932  __swig_destroy__ = _IMP_bff.delete_DecayLifetimeHandler
2933 
2934  def __str__(self):
2935  r"""__str__(DecayLifetimeHandler self) -> std::string"""
2936  return _IMP_bff.DecayLifetimeHandler___str__(self)
2937 
2938  def __repr__(self):
2939  r"""__repr__(DecayLifetimeHandler self) -> std::string"""
2940  return _IMP_bff.DecayLifetimeHandler___repr__(self)
2941 
2942  @staticmethod
2943  def get_from(o):
2944  return _object_cast_to_DecayLifetimeHandler(o)
2945 
2946  abs_lifetime_spectrum = property(_IMP_bff.DecayLifetimeHandler_abs_lifetime_spectrum_get, _IMP_bff.DecayLifetimeHandler_abs_lifetime_spectrum_set, doc=r"""abs_lifetime_spectrum : bool""")
2947  use_amplitude_threshold = property(_IMP_bff.DecayLifetimeHandler_use_amplitude_threshold_get, _IMP_bff.DecayLifetimeHandler_use_amplitude_threshold_set, doc=r"""use_amplitude_threshold : bool""")
2948  amplitude_threshold = property(_IMP_bff.DecayLifetimeHandler_amplitude_threshold_get, _IMP_bff.DecayLifetimeHandler_amplitude_threshold_set, doc=r"""amplitude_threshold : double""")
2949  lifetime_spectrum = property(_IMP_bff.DecayLifetimeHandler_lifetime_spectrum_get, _IMP_bff.DecayLifetimeHandler_lifetime_spectrum_set, doc=r"""lifetime_spectrum : std::vector<(double,std::allocator<(double)>)>""")
2950 
2951 # Register DecayLifetimeHandler in _IMP_bff:
2952 _IMP_bff.DecayLifetimeHandler_swigregister(DecayLifetimeHandler)
2953 
2954 DecayModifiers=list
2955 _plural_types.append("DecayModifiers")
2956 _value_types.append("DecayModifier")
2957 
2958 class DecayModifier(DecayRange):
2959  r"""Proxy of C++ IMP::bff::DecayModifier class."""
2960 
2961  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2962 
2963  def __init__(self, *args, **kwargs):
2964  raise AttributeError("No constructor defined - class is abstract")
2965 
2966  def set_data(self, v):
2967  r"""set_data(DecayModifier self, DecayCurve v)"""
2968  return _IMP_bff.DecayModifier_set_data(self, v)
2969 
2970  def get_data(self):
2971  r"""get_data(DecayModifier self) -> DecayCurve"""
2972  return _IMP_bff.DecayModifier_get_data(self)
2973 
2974  def set(self, data, start=0, stop=-1, active=True):
2975  r"""set(DecayModifier self, DecayCurve data, int start=0, int stop=-1, bool active=True)"""
2976  return _IMP_bff.DecayModifier_set(self, data, start, stop, active)
2977 
2978  def resize(self, n, v=0.0):
2979  r"""resize(DecayModifier self, size_t n, double v=0.0)"""
2980  return _IMP_bff.DecayModifier_resize(self, n, v)
2981 
2982  def add(self, out):
2983  r"""add(DecayModifier self, DecayCurve out)"""
2984  return _IMP_bff.DecayModifier_add(self, out)
2985  __swig_destroy__ = _IMP_bff.delete_DecayModifier
2986 
2987  def __str__(self):
2988  r"""__str__(DecayModifier self) -> std::string"""
2989  return _IMP_bff.DecayModifier___str__(self)
2990 
2991  def __repr__(self):
2992  r"""__repr__(DecayModifier self) -> std::string"""
2993  return _IMP_bff.DecayModifier___repr__(self)
2994  active = property(_IMP_bff.DecayModifier_active_get, _IMP_bff.DecayModifier_active_set, doc=r"""active : bool""")
2995 
2996  data = property(get_data, set_data)
2997 
2998 
2999  def __call__(self, *args, **kwargs):
3000  self.add(*args, **kwargs)
3001 
3002 
3003 # Register DecayModifier in _IMP_bff:
3004 _IMP_bff.DecayModifier_swigregister(DecayModifier)
3005 
3006 DecayConvolutions=list
3007 _plural_types.append("DecayConvolutions")
3008 _value_types.append("DecayConvolution")
3009 
3010 class DecayConvolution(DecayModifier):
3011  r"""Proxy of C++ IMP::bff::DecayConvolution class."""
3012 
3013  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3014  FAST_PERIODIC_TIME = _IMP_bff.DecayConvolution_FAST_PERIODIC_TIME
3015 
3016  FAST_TIME = _IMP_bff.DecayConvolution_FAST_TIME
3017 
3018  FAST_PERIODIC = _IMP_bff.DecayConvolution_FAST_PERIODIC
3019 
3020  FAST = _IMP_bff.DecayConvolution_FAST
3021 
3022  FAST_AVX = _IMP_bff.DecayConvolution_FAST_AVX
3023 
3024  FAST_PERIODIC_AVX = _IMP_bff.DecayConvolution_FAST_PERIODIC_AVX
3025 
3026 
3027  @staticmethod
3028  def compute_corrected_irf(irf, corrected_irf, irf_shift_channels, irf_background_counts):
3029  r"""compute_corrected_irf(DecayCurve irf, DecayCurve corrected_irf, double irf_shift_channels, double irf_background_counts)"""
3030  return _IMP_bff.DecayConvolution_compute_corrected_irf(irf, corrected_irf, irf_shift_channels, irf_background_counts)
3031 
3032  @staticmethod
3033  def compute_mean_lifetime(irf_histogram, decay_histogram, micro_time_resolution):
3034  r"""compute_mean_lifetime(VectorDouble irf_histogram, VectorDouble decay_histogram, double micro_time_resolution) -> double"""
3035  return _IMP_bff.DecayConvolution_compute_mean_lifetime(irf_histogram, decay_histogram, micro_time_resolution)
3036 
3037  def set_irf(self, v):
3038  r"""set_irf(DecayConvolution self, DecayCurve v)"""
3039  return _IMP_bff.DecayConvolution_set_irf(self, v)
3040 
3041  def get_irf(self):
3042  r"""get_irf(DecayConvolution self) -> DecayCurve"""
3043  return _IMP_bff.DecayConvolution_get_irf(self)
3044 
3045  def get_mean_lifetime(self, decay):
3046  r"""get_mean_lifetime(DecayConvolution self, DecayCurve decay) -> double"""
3047  return _IMP_bff.DecayConvolution_get_mean_lifetime(self, decay)
3048 
3049  def set(self, *args, **kwargs):
3050  r"""set(DecayConvolution self, int convolution_method=FAST_PERIODIC_TIME, double excitation_period=100, double irf_shift_channels=0.0, double irf_background_counts=0)"""
3051  return _IMP_bff.DecayConvolution_set(self, *args, **kwargs)
3052 
3053  def __init__(self, *args, **kwargs):
3054  r"""__init__(DecayConvolution self, DecayLifetimeHandler lifetime_handler=None, DecayCurve instrument_response_function=None, int convolution_method=FAST, double excitation_period=100, double irf_shift_channels=0.0, double irf_background_counts=0, int start=0, int stop=-1, bool active=True) -> DecayConvolution"""
3055  _IMP_bff.DecayConvolution_swiginit(self, _IMP_bff.new_DecayConvolution(*args, **kwargs))
3056  __swig_destroy__ = _IMP_bff.delete_DecayConvolution
3057 
3058  def __str__(self):
3059  r"""__str__(DecayConvolution self) -> std::string"""
3060  return _IMP_bff.DecayConvolution___str__(self)
3061 
3062  def __repr__(self):
3063  r"""__repr__(DecayConvolution self) -> std::string"""
3064  return _IMP_bff.DecayConvolution___repr__(self)
3065  corrected_irf = property(_IMP_bff.DecayConvolution_corrected_irf_get, doc=r"""corrected_irf : r.IMP::bff::DecayCurve""")
3066  convolution_method = property(_IMP_bff.DecayConvolution_convolution_method_get, _IMP_bff.DecayConvolution_convolution_method_set, doc=r"""convolution_method : int""")
3067  excitation_period = property(_IMP_bff.DecayConvolution_excitation_period_get, _IMP_bff.DecayConvolution_excitation_period_set, doc=r"""excitation_period : double""")
3068  irf_shift_channels = property(_IMP_bff.DecayConvolution_irf_shift_channels_get, _IMP_bff.DecayConvolution_irf_shift_channels_set, doc=r"""irf_shift_channels : double""")
3069  irf_background_counts = property(_IMP_bff.DecayConvolution_irf_background_counts_get, _IMP_bff.DecayConvolution_irf_background_counts_set, doc=r"""irf_background_counts : double""")
3070 
3071  irf = property(get_irf, set_irf)
3072 
3073 
3074 # Register DecayConvolution in _IMP_bff:
3075 _IMP_bff.DecayConvolution_swigregister(DecayConvolution)
3076 
3077 DecayPatterns=list
3078 _plural_types.append("DecayPatterns")
3079 _value_types.append("DecayPattern")
3080 
3081 class DecayPattern(DecayModifier):
3082  r"""Proxy of C++ IMP::bff::DecayPattern class."""
3083 
3084  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3085 
3086  def __init__(self, constant_offset=0.0, pattern=None, pattern_fraction=0.0, start=0, stop=-1, active=True):
3087  r"""__init__(DecayPattern self, double constant_offset=0.0, DecayCurve pattern=None, double pattern_fraction=0.0, int start=0, int stop=-1, bool active=True) -> DecayPattern"""
3088  _IMP_bff.DecayPattern_swiginit(self, _IMP_bff.new_DecayPattern(constant_offset, pattern, pattern_fraction, start, stop, active))
3089 
3090  def __str__(self):
3091  r"""__str__(DecayPattern self) -> std::string"""
3092  return _IMP_bff.DecayPattern___str__(self)
3093 
3094  def __repr__(self):
3095  r"""__repr__(DecayPattern self) -> std::string"""
3096  return _IMP_bff.DecayPattern___repr__(self)
3097  pattern = property(_IMP_bff.DecayPattern_pattern_get, _IMP_bff.DecayPattern_pattern_set, doc=r"""pattern : p.IMP::bff::DecayCurve""")
3098  pattern_fraction = property(_IMP_bff.DecayPattern_pattern_fraction_get, _IMP_bff.DecayPattern_pattern_fraction_set, doc=r"""pattern_fraction : double""")
3099  constant_offset = property(_IMP_bff.DecayPattern_constant_offset_get, _IMP_bff.DecayPattern_constant_offset_set, doc=r"""constant_offset : double""")
3100  __swig_destroy__ = _IMP_bff.delete_DecayPattern
3101 
3102 # Register DecayPattern in _IMP_bff:
3103 _IMP_bff.DecayPattern_swigregister(DecayPattern)
3104 
3105 DecayPileups=list
3106 _plural_types.append("DecayPileups")
3107 _value_types.append("DecayPileup")
3108 
3109 class DecayPileup(DecayModifier):
3110  r"""Proxy of C++ IMP::bff::DecayPileup class."""
3111 
3112  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3113 
3114  def __init__(self, *args, **kwargs):
3115  r"""__init__(DecayPileup self, DecayCurve data, char const * pile_up_model="coates", double repetition_rate=100, double instrument_dead_time=120, int start=0, int stop=-1, bool active=True) -> DecayPileup"""
3116  _IMP_bff.DecayPileup_swiginit(self, _IMP_bff.new_DecayPileup(*args, **kwargs))
3117 
3118  def __str__(self):
3119  r"""__str__(DecayPileup self) -> std::string"""
3120  return _IMP_bff.DecayPileup___str__(self)
3121 
3122  def __repr__(self):
3123  r"""__repr__(DecayPileup self) -> std::string"""
3124  return _IMP_bff.DecayPileup___repr__(self)
3125  instrument_dead_time = property(_IMP_bff.DecayPileup_instrument_dead_time_get, _IMP_bff.DecayPileup_instrument_dead_time_set, doc=r"""instrument_dead_time : double""")
3126  repetition_rate = property(_IMP_bff.DecayPileup_repetition_rate_get, _IMP_bff.DecayPileup_repetition_rate_set, doc=r"""repetition_rate : double""")
3127  pile_up_model = property(_IMP_bff.DecayPileup_pile_up_model_get, _IMP_bff.DecayPileup_pile_up_model_set, doc=r"""pile_up_model : std::string""")
3128  __swig_destroy__ = _IMP_bff.delete_DecayPileup
3129 
3130 # Register DecayPileup in _IMP_bff:
3131 _IMP_bff.DecayPileup_swigregister(DecayPileup)
3132 
3133 DecayLinearizations=list
3134 _plural_types.append("DecayLinearizations")
3135 _value_types.append("DecayLinearization")
3136 
3137 class DecayLinearization(DecayModifier):
3138  r"""Proxy of C++ IMP::bff::DecayLinearization class."""
3139 
3140  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3141 
3142  def set_linearization_table(self, v):
3143  r"""set_linearization_table(DecayLinearization self, DecayCurve v)"""
3144  return _IMP_bff.DecayLinearization_set_linearization_table(self, v)
3145 
3146  def get_linearization_table(self):
3147  r"""get_linearization_table(DecayLinearization self) -> DecayCurve"""
3148  return _IMP_bff.DecayLinearization_get_linearization_table(self)
3149 
3150  def __init__(self, linearization_table, start, stop, active=True, n_window=5):
3151  r"""__init__(DecayLinearization self, DecayCurve linearization_table, int start, int stop, bool active=True, int n_window=5) -> DecayLinearization"""
3152  _IMP_bff.DecayLinearization_swiginit(self, _IMP_bff.new_DecayLinearization(linearization_table, start, stop, active, n_window))
3153 
3154  def __str__(self):
3155  r"""__str__(DecayLinearization self) -> std::string"""
3156  return _IMP_bff.DecayLinearization___str__(self)
3157 
3158  def __repr__(self):
3159  r"""__repr__(DecayLinearization self) -> std::string"""
3160  return _IMP_bff.DecayLinearization___repr__(self)
3161  __swig_destroy__ = _IMP_bff.delete_DecayLinearization
3162 
3163 # Register DecayLinearization in _IMP_bff:
3164 _IMP_bff.DecayLinearization_swigregister(DecayLinearization)
3165 
3166 DecayScales=list
3167 _plural_types.append("DecayScales")
3168 _value_types.append("DecayScale")
3169 
3170 class DecayScale(DecayModifier):
3171  r"""Proxy of C++ IMP::bff::DecayScale class."""
3172 
3173  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3174 
3175  def set_blank_outside(self, v):
3176  r"""set_blank_outside(DecayScale self, double v)"""
3177  return _IMP_bff.DecayScale_set_blank_outside(self, v)
3178 
3179  def get_blank_outside(self):
3180  r"""get_blank_outside(DecayScale self) -> bool"""
3181  return _IMP_bff.DecayScale_get_blank_outside(self)
3182 
3183  def set(self, data=None, constant_background=0.0, start=0, stop=-1, active=True, blank_outside=True):
3184  r"""set(DecayScale self, DecayCurve data=None, double constant_background=0.0, int start=0, int stop=-1, bool active=True, bool blank_outside=True)"""
3185  return _IMP_bff.DecayScale_set(self, data, constant_background, start, stop, active, blank_outside)
3186 
3187  def __init__(self, data=None, constant_background=0.0, start=0, stop=-1, active=True, blank_outside=True):
3188  r"""__init__(DecayScale self, DecayCurve data=None, double constant_background=0.0, int start=0, int stop=-1, bool active=True, bool blank_outside=True) -> DecayScale"""
3189  _IMP_bff.DecayScale_swiginit(self, _IMP_bff.new_DecayScale(data, constant_background, start, stop, active, blank_outside))
3190 
3191  def __str__(self):
3192  r"""__str__(DecayScale self) -> std::string"""
3193  return _IMP_bff.DecayScale___str__(self)
3194 
3195  def __repr__(self):
3196  r"""__repr__(DecayScale self) -> std::string"""
3197  return _IMP_bff.DecayScale___repr__(self)
3198  number_of_photons = property(_IMP_bff.DecayScale_number_of_photons_get, doc=r"""number_of_photons : double""")
3199  constant_background = property(_IMP_bff.DecayScale_constant_background_get, _IMP_bff.DecayScale_constant_background_set, doc=r"""constant_background : double""")
3200  __swig_destroy__ = _IMP_bff.delete_DecayScale
3201 
3202 # Register DecayScale in _IMP_bff:
3203 _IMP_bff.DecayScale_swigregister(DecayScale)
3204 
3205 DecayScores=list
3206 _plural_types.append("DecayScores")
3207 _value_types.append("DecayScore")
3208 
3209 class DecayScore(DecayRange):
3210  r"""Proxy of C++ IMP::bff::DecayScore class."""
3211 
3212  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3213 
3214  def get_model(self):
3215  r"""get_model(DecayScore self) -> DecayCurve"""
3216  return _IMP_bff.DecayScore_get_model(self)
3217 
3218  def set_model(self, v):
3219  r"""set_model(DecayScore self, DecayCurve v)"""
3220  return _IMP_bff.DecayScore_set_model(self, v)
3221 
3222  def get_data(self):
3223  r"""get_data(DecayScore self) -> DecayCurve"""
3224  return _IMP_bff.DecayScore_get_data(self)
3225 
3226  def set_data(self, v):
3227  r"""set_data(DecayScore self, DecayCurve v)"""
3228  return _IMP_bff.DecayScore_set_data(self, v)
3229 
3230  def get_weighted_residuals(self):
3231  r"""get_weighted_residuals(DecayScore self) -> VectorDouble"""
3232  return _IMP_bff.DecayScore_get_weighted_residuals(self)
3233 
3234  def get_score(self, start=0, stop=-1, score_type=None):
3235  r"""get_score(DecayScore self, int start=0, int stop=-1, char const * score_type=None) -> double"""
3236  return _IMP_bff.DecayScore_get_score(self, start, stop, score_type)
3237 
3238  def set(self, *args, **kwargs):
3239  r"""set(DecayScore self, DecayCurve model, DecayCurve data, std::string score_type="poisson", int start=0, int stop=-1)"""
3240  return _IMP_bff.DecayScore_set(self, *args, **kwargs)
3241 
3242  def __init__(self, *args, **kwargs):
3243  r"""__init__(DecayScore self, DecayCurve model=None, DecayCurve data=None, std::string score_type="poisson", int start=0, int stop=-1) -> DecayScore"""
3244  _IMP_bff.DecayScore_swiginit(self, _IMP_bff.new_DecayScore(*args, **kwargs))
3245  __swig_destroy__ = _IMP_bff.delete_DecayScore
3246 
3247  def __str__(self):
3248  r"""__str__(DecayScore self) -> std::string"""
3249  return _IMP_bff.DecayScore___str__(self)
3250 
3251  def __repr__(self):
3252  r"""__repr__(DecayScore self) -> std::string"""
3253  return _IMP_bff.DecayScore___repr__(self)
3254  score_type = property(_IMP_bff.DecayScore_score_type_get, _IMP_bff.DecayScore_score_type_set, doc=r"""score_type : std::string""")
3255  score = property(_IMP_bff.DecayScore_score_get, doc=r"""score : double""")
3256 
3257  model = property(get_model, set_model)
3258 
3259 
3260  data = property(get_data, set_data)
3261 
3262 
3263  weighted_residuals = property(
3264  lambda x: np.array(x.get_weighted_residuals())
3265  )
3266 
3267 
3268 # Register DecayScore in _IMP_bff:
3269 _IMP_bff.DecayScore_swigregister(DecayScore)
3270 
3271 def get_module_name():
3272  r"""get_module_name() -> std::string const"""
3273  return _IMP_bff.get_module_name()
3274 
3275 def get_module_version():
3276  r"""get_module_version() -> std::string const"""
3277  return _IMP_bff.get_module_version()
3278 
3279 def get_example_path(fname):
3280  r"""get_example_path(std::string fname) -> std::string"""
3281  return _IMP_bff.get_example_path(fname)
3282 
3283 def get_data_path(fname):
3284  r"""get_data_path(std::string fname) -> std::string"""
3285  return _IMP_bff.get_data_path(fname)
3286 
3287 from . import _version_check
3288 _version_check.check_version(get_module_version())
3289 __version__ = get_module_version()
3290 
3291 
void decay_fconv_per_cs(double *fit, double *x, double *lamp, int numexp, int stop, int n_points, double period, int conv_stop, double dt)
Convolve lifetime spectrum - fast convolution, high repetition rate, with convolution stop...
void decay_fconv_avx(double *fit, double *x, double *lamp, int numexp, int start, int stop, double dt=0.05)
Convolve lifetime spectrum with instrument response (fast convolution, AVX optimized for large lifeti...
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:80
void decay_rescale_w_bg(double *fit, double *decay, double *e_sq, double bg, double *scale, int start, int stop)
Scale model function to the data (with weights and background)
Various classes to hold sets of particles.
void decay_fconv_cs_time_axis(double *inplace_output, int n_output, double *time_axis, int n_time_axis, double *irf, int n_irf, double *lifetime_spectrum, int n_lifetime_spectrum, int convolution_start=0, int convolution_stop=-1)
Make CGAL functionality available to IMP.
void decay_rescale_w(double *fit, double *decay, double *w_sq, double *scale, int start, int stop)
Scale model function to the data (with weights).
void decay_add_pile_up_to_model(double *model, int n_model, double *data, int n_data, double repetition_rate, double instrument_dead_time, double measurement_time, std::string pile_up_model="coates", int start=0, int stop=-1)
Add a pile-up distortion to the model function.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Composable functors to implement scores via compile-time composition.
double av_distance(const AV &a, const AV &b, double forster_radius=52.0, int distance_type=DYE_PAIR_DISTANCE_MEAN, int n_samples=10000)
Computes the distance to another accessible volume.
void decay_rescale(double *fit, double *decay, double *scale, int start, int stop)
Scale model function to the data (old version).
void decay_fconv(double *fit, double *x, double *lamp, int numexp, int start, int stop, double dt=0.05)
Convolve lifetime spectrum with instrument response (fast convolution, low repetition rate) ...
void decay_fconv_per(double *fit, double *x, double *lamp, int numexp, int start, int stop, int n_points, double period, double dt=0.05)
Convolve lifetime spectrum with instrument response (fast convolution, high repetition rate) ...
void decay_shift_lamp(double *lampsh, double *lamp, double ts, int n_points, double out_value=0.0)
shift instrument response function
Code to compute statistical measures.
std::vector< double > av_distance_distribution(const AV &av1, const AV &av2, std::vector< double > axis, int n_samples=10000)
Compute the distance to another accessible volume.
Class for sampling a density map from particles.
Common base class for heavy weight IMP objects.
Definition: Object.h:111
void decay_sconv(double *fit, double *p, double *lamp, int start, int stop)
Convolve fluorescence decay curve with irf.
Basic utilities for handling cryo-electron microscopy 3D density maps.
void decay_fconv_per_cs_time_axis(double *model, int n_model, double *time_axis, int n_time_axis, double *irf, int n_irf, double *lifetime_spectrum, int n_lifetime_spectrum, int convolution_start=0, int convolution_stop=-1, double period=100.0)
void decay_fconv_ref(double *fit, double *x, double *lamp, int numexp, int start, int stop, double tauref, double dt=0.05)
Convolve lifetime spectrum - fast convolution with reference compound decay.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
void write_path_map(PathMap *m, std::string filename, int value_type, const std::pair< float, float > bounds=std::pair< float, float >(std::numeric_limits< float >::min(), std::numeric_limits< float >::max()), const std::string &feature_name="")
Writes a path map to a file.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
void decay_fconv_per_avx(double *fit, double *x, double *lamp, int numexp, int start, int stop, int n_points, double period, double dt=0.05)
Convolve lifetime spectrum with instrument response (fast convolution, high repetition rate)...
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void discriminate_small_amplitudes(double *lifetime_spectrum, int n_lifetime_spectrum, double amplitude_threshold)
std::vector< double > av_random_distances(const AV &av1, const AV &av2, int n_samples=10000)
Random sampling over AV/AV distances.
IMP::ParticleIndex search_labeling_site(const IMP::core::Hierarchy &hier, std::string json_str="", const nlohmann::json &json_data=nlohmann::json())
Find the particle index of a labeling site.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
ParticleIndexes get_indexes(const ParticlesTemp &ps)
Get the indexes from a list of particles.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:72
std::string get_module_version()
Return the version of this module, as a string.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:56
int mod_p(int a, int n)
Compute the modulo of a number with respect to a positive integer.
Definition: DecayRoutines.h:48